A smear campaign.

If we can get people to believe that vaccines are bad for you, and Global Warming is a hoax, then it should be easy to convince people that using portals causes 'X'.

Now 'X' can be anything. The only prerequisite is that it causes fear, and that there is a propaganda machine or echo chamber people use to back it up. Here are some ideas of what 'X' could be.

Using portals:

1. Makes you infertile;




2. Lowers your IQ;




3. Causes some disease;




4. Exposes you to a specific chemical or radiation that people are afraid of;




5. Changes your genes;




6. Ages you.

None of these things have to actually be true. You just have to put fear in peoples minds and then a lot of people will avoid it. You can maintain this fear with mass media.

People aren't great at assessing the relative safety of transport methods, more people are afraid of flying than getting the train or going by car yet statistically it's safer than either.

Substitute "I'm afraid the plane will fall out of the sky" for "I'm afraid I'll step into the portal and not come out the other end" and there you go!

A) People have religious reservations about the portals, especially if they espouse a different religion than the one that controls the portals.

B) While statistically safer, the portals' occasional failures are gruesome and widely publicized.

C) The portals are controlled by the government --you have to give up a lot of your privacy and go through a strict process to access them.

D) The portals have unpleasant side effects (bad dreams for months?)

I've poached this concept from the book The Stars my Destination by Alfred Bester, to answer a similar question before.

For the elite, traditional transportation is considered a conspicuous luxury.

In the story, humankind have developed the capability to teleport or jaunte themselves to any location they know about or have been to before, but can't, for instance, teleport into space or any secret or private area. But the fabulously and filthy rich are often seen using helicopters, flying cars, or even steam trains to show up at business meetings, events, or soirees (the more archaic, the better). The delicious irony of this is that their time is so much more valuable than anyone else's, and therefore they can afford to make others wait for them. In this world of instant transmission, they're not wasting everyone else's time, they're just reinforcing their own importance in the system.

I can imagine in your world that the obscenely wealthy might be seen travelling upon pleasure barges or in caravans with their finest treasures and elite military in tow. Unlike common folk, there's nowhere they need to be quickly, and once they arrive, it's a real special occasion. Or maybe their flaunting of their wealth is even seen as thumbing their noses at the church.

One theory of possible teleportation essentially entails copying your entire bodys quantum state and printing it on the other side.

The moral question becomes what to do with the original, disintegration? Then there is the question of is the copy a copy or a continuation of the original.

So to answer your question, people would be adverse to the notion of using portals because they don't want to be disintegrated even though they may still live.

There are a variety of reasons for why it may be more desirable to travel by ship or caravan.

1. Lack of faith


2. Misinformation


3. Desire for adventure


4. Unwillingness to leave their life in "God's Hands" regardless of faith


5. General lack of accessibility due to other reasons

Lack of Faith

If you don't believe in God, do you think you're going to be as likely to take these supposedly miraculous routes of transportation? Surely there must be a trick to the process or some kind of con associated with it, no? Okay, let's assume the unbeliever was still willing to use the Gates... do you believe the church would let them? Sure, they may be required to leave access open and free for the believers, but faith may be a requirement the church demands from all those who wish to use it. Even if the church doesn't outright demand as such, people may avoid it simply because they think the church will demand it. After all, how many atheists do you see going to a church event where there's free food? Usually not many unless they're being dragged there by a member of that church. These portals are in City-State-size churches, so surely nonbelievers will be more likely to steer clear even despite it being free. Not to say there won't be any nonbelievers, but you'll find a stark contrast in the percentage of believers using the portals compared to the world population and the number of nonbelievers.

Misinformation

Look at vaccines for proof of this. Sure, a minority of vaccines can cause issues for people. They can cause allergic reactions in some and might have a small part in causing other issues. For the vast majority, it's far safer to be vaccinated than it is to go without, though. But yet there are anti-vaccination people screaming that it does in fact cause a whole slew of disorders that there's no evidence for. The louder their voices get, the more doubt in vaccines grows.

The same is true for these portals. There are people claiming that if you use them terrible things will happen.

After hearing all the bad things that can happen, alongside the fact it's an absolute lottery on if they happen (and not a lottery that you want to win), of course they wouldn't want to risk it. Sure, it might be safer if you listen to the church who likely has a vested interest in people using the portals, but is it safe enough to risk... that?

Desire for adventure

Maybe it's the simple fact it is safer that keeps people from using the portals? After all, humans love adventure. Giving it up might be fine for some, but life isn't so much about the destination, just how you get there. If you don't enjoy the journey, what value is there in life seeing as it itself is a journey with death being the inevitable destination. The Goal of All Life Is Death, after all. What is life without a journey, and what is a journey if not an adventure?

Unwillingness to leave their life in "God's Hands" regardless of faith

This sort of ties back to #2. Regardless of if you are devout or not, leaving your life completely in "God's Hands" is a terrifying prospect. What if something goes wrong? What if I don't go to the right place? What if those rumors are true? What if... what if... WHAT IF...? It's easy to have faith, but acting on that faith is a whole other manner. Look at the biblical cases of people who had faith being asked to act on it, but failed. Jonah and the Whale being one of the most classic examples. He was told to go to a town of sinners and save them. Instead, he went the other direction. God had him swallowed by a big fish (commonly attributed to a whale). It's not easy for a person to do something that scares them, especially not when you tell them they have no control over what happens. If you travel in a caravan and get robbed, you at least have the choice to fight back. If you fight back well enough, no consequences will happen. You may even gain something from the event aside from just experience! In a medieval world, the more property you have, the better, so it'd be worth it if you had confidence in your skills or guards. If you take the portals, you miss out on the opportunity to grow and you are taking a risk you have no hope of stopping once it starts.

General lack of accessibility due to other reasons

Perhaps the portals and surrounding land are safe, but what about the roads leading there? Nothing guarantees bandits and thieves won't ambush you as you make your way to the portal and since that is where the highest traffic would be, that is where it's actually the most dangerous. Sure, once you get to the portals or surrounding lands it's the safest means of travel, but if you don't live close enough to the portal, it's too risky. Even if you live close enough to a portal, if your destination is outside the territory under the church's protection, then those roads are at risk of bandits and thieves. The portals are only a safer option in limited circumstances.

Maybe the church doesn't charge for the use of the portals, but the church could charge a toll or tax for entering the land. Sure they'd call it an optional donation, but in reality it would act as an obligatory offering if you want decent service or to avoid being thrown in prison for being in violation of one of the many outdated holy laws that govern the land, such as "Thou must not wear socks with sandals!"

Perhaps, there could be allergies, cultural traditions, or other environmental features that prevent a subsection of the population from using the portals. It may not even have to do with the portals themselves, but the things involving the land around the portals such as a pollen allergy and it just happens that the portals are surrounded by gardens the church refers to as "Edens", alongside the accompanying allergic reaction that comes to those who venture near. Maybe the areas around the portal have incense burning 24/7, and those incenses cause allergies. Maybe if you get sick or start to feel unwell near the portals or within the church's borders, they arrest you for being an unrepentant sinner and your sickness and unease is god's way of alerting them to you lacking right to use the portal.

Finally, maybe there's even a requirement that you must wait so long to use the portals again. So, once you go through one side, you're stuck on the other for X number of days/weeks/months before you can return home. In that case, it may just be better, unless you are rich and own a home on each side of the portal, to just take the long way there and the portal back if there's an emergency.

How do the portals work? No-one knows, and people don't like that, people like to understand how they're getting from point A to point B so many will take a slower but clearly understood transport instead. It may also be that while people do understand the how they think its unnatural, think Bones and the transporters in Star Trek; he understands how they work perfectly and he refuses to go anywhere near them as a result.

It's expensive.

These portals are very useful, and someone is going to find a way to monetize them. The powers-that-be in your setting control access to these portals and charge a fee for their use. Not everyone can afford to travel by portal, so those that cannot have to go the slow way. Saving months of dangerous travel time has great value, so these portal trips aren't going to be cheap.

Side note: This answer was edited after careful reading of the question.

Dangerous Roads

The portals are free - but that doesn't mean using them has no cost.

Think of a person who wants to go from A to C. This trip takes 15 days. That's 15 days worth of food, water, animals, protection, etc.

B is the place where the portal is. The trip from A to B takes 5 days, which is a better bargain, by far. However, the road to B is far more dangerous than going straight to C.

Would your risk losing your precious cargo over a shorter trip?

Side Effects

The gods are pretty confident in their ability to control space - even though that is a skill they've yet to master. This means that teleportation isn't quite... perfect.

The direct result of that would be you coming out of the portal completely covered in a thick, dark, putrid goo every single time you get out of a portal.

This wouldn't be considered dangerous because the goo is completely harmless - but it would still be a nuisance anyway.

The beauty of this is that you can think of any kind of mild side effect (like partial hearing or sight loss) and just say that it wears off in a couple of hours/days.

User Mistake

Scholars and wizards might know how to use them perfectly. But will Wyatt, an uninstructed farmer from the edges of the empire, know how to do it as well?

Maybe there's a little individual aspect to this type of travelling (like thinking REALLY hard about the place you want to go) that could result in people ending up in odd places or even disappearing altogether.

There aren't THAT many portals

You said gifts from gods in a world 25 times bigger than Earth. I'm no expert in godly gifts but I know that the earth is freaking huge already.

Assuming your gods are not THAT benevolent, I'd say that there aren't enough portals to make it actually be a common thing. Sure, every major city has it's own portal (maybe even more than one).

But there are stil thousands of smaller cities, villages and just plain non-urban populated areas spread around your insanely big planet. The sheer fact that only the big cities have these portals in a world as huge as yours is enough reason to say they're not that much common.

One major reason that hasn't been mentioned yet:

The church must (largely) maintain its neutrality, and so must deny passage to the armies (and probably supplies for same) of all nations. The advantage of such a network should be obvious to any competent general, and so to avoid being used to prosecute wars the church will deny transit to all large groups of fighting men. This also protects their dominance of the network itself, because letting an army into the transit area risks it being captured.

So if you're fighting a war, your army needs to take the long way around.

D&D 5e handles this well. I'm playing a campaign that involves a network of Teleportation Circles that let you easily go place to place. In fact, you can teleport from anywhere on the same plane of existence to one, but we can ignore that for the purposes of this question. The only drawback? You must spend 50 goals worth of materials (arcane chalk) to draw one at your location (even if you have a permanent Circle nearby) and open it.

To translate that to this: They must be opened, and there is material cost associated with opening them. The religious group could call it a tribute to their god.

Some people may be allergic to mana. The portals use a lot of mana to work. For someone who is allergic, taking a portal would be like someone allergic to polen having a pound of condensed polen shoved up their nostrils.

Also think of people who are afraid of getting into plane in our world. Planes are statistically safer than cars, yet there are people who are afraid to fly but who are ok with cars.

Finally, due to clerical error, God thinks that I have been dead since 2006. If I had to travel anywhere through any methods, I wouldn't want to take a divine road and risk Him noticing me there, finding out about the mistake and wanting to fix it.

Religion doesn't always sit or play well with everyone.

"The religious organization of this world control these states as well as the portals they are built around. They are considered a separate power directly under God's authority."

There's your answer. Believers in a different religion might see the use of those portals as heresy. Non-believers might be denied access for heresy, because they don't think they have anything to do with so-called 'gods'. Or they might view the organization (rightly or wrongly) as corrupt, and be unwilling to patronize the portals as a result.

1. Religion - you must have be good member of church to be able to use portals.


2. Law - you must have clean record and they check your items - so no stolen, shady goods, no-no lists.


3. Fees - you must pay fees. For people depending on class or reputation with church. And items by weight or type.


4. Limits - you can move limited amount by size or weight with different level of access. Some things may be impossible to move via gates.


5. Fun of travel - Meaby you just want to explore the world and have your adventure.


6. Dangers - some people may have problems with teleportation. Low random chance or some group of people.


7. Fears - like talks about people living less or whatever BS.


8. World is big - most travel is between 95-99% of villages, towns, cities that do not have portals. In addition, that means merchants have sacks of gold to be made, moving caravans between hundreds of small and big settlements with no portals.

Fear of divine judgement

These portals [...] are considered sacred, given to humanity by the gods in an act of generosity. Therefore, these cities are untouchable by crime or invasion by outside forces.

Perhaps the religion of your world puts a lot of emphasis on guilt and making oneself "worthy" of the gods before praying or practicing rituals.

The most fervent participant of your religion may then fear that if they are to take advantage of the god's blessing without deserving it, they are exposing themselves to punishment, and would be reluctant to use it before they have purified their soul in whatever way their religion dictates.

Most fictional portals blatantly disregard the First Law of Thermodynamics. Put one portal at the top of a mountain, one at the bottom, have water flowing between them and turbine or two, and you have a perpetual motion machine. Infinite free energy.

I suspect, with a more realistic portal, that spacetime would warp around the portals, balancing out the differences in potential energy. If you got too close to the portal at the top of the mountain you would get sucked in with extreme force and would be reduced to a gooey mess coming out the other side. Going through the portal the other way would require as much energy as climbing the mountain and would be impossible without advanced technology.

Perhaps these portals are not all at the same height, and the force sucking downwards is too much to bear unless you are quite fit. Perhaps some portals are at similar heights and relatively safe, while others are at wildly different heights and the portals are almost unusable.

Portals are overcrowded

Only so many people can go through a portal at a time, and there are lots of people who want to use them. With only one portal available for each continent, traveling through a portal will usually require a lot of waiting around in line, and there might even be a whole system of bureaucratic red tape to go through to reserve your appointment, properly identify yourself (so that no one jumps the queue), etc.

Portals are too far away

There's only one portal per continent. If I wanted to travel from London to New York, and the portals for those two continents were in Los Angeles and Rome, then it might be easier for me to just take a ship across the Atlantic than to make the overland trek to the nearest portal and then from there to my destination.

Several options:

1. 
   

   Perhaps they can only transport significant quantities of material with less than a certain atomic weight? Say 20 (Calcium). So humans are unaffected (iron in our hemoglobin and other trace minerals make it through). But you won't be taking your coin purse with gold, silver, copper, etc with you. Nor iron weapons or horseshoes, bridles, etc.

   
   
   

   So wood, grains, and lots of other products (Carbon has an atomic weight of 12) can go through, and animals/people but to travel fully instantaneously you need to be rich enough to make arrangements at this end to have someone provide you with these things at the far end. Otherwise, you have to ship it ahead (again, that takes a fair amount of money to reliably ship something) or you have to travel the old-fashioned way and carry it yourself.

   
   



2. Perhaps they have a volume restriction? For example, the portals might only be large enough to fit something about the size of a horse and will only accept (stay open long enough) something about the length of two horses. (Anything longer will get chopped off.)




3. Perhaps, as a part of the portal operations' extreme security, everything that goes through is strictly examined. They don't allow items forbidden by their faith through. Also, if you're a merchant, say, your competitors could review the records of everything -- including the quantity and kind of all of your wares plus how much gold you have -- that you took through.




4. Side Effects. Perhaps there's some level of radiation involved and living things can only make a certain number/distance of trips within a period of given time before you risk side effects.

People don't just go places for the sake of going places

All the cities with portal exits are essentially one city, right? Travel and communication between them is virtually instantaneous and they're all ruled by one government. Travel to the cities is traditional - by road, sea, river, or canal. People who live more than 50-100 miles away from one of the cities might never go that far in a lifetime, unless they have a professional reason to travel:

• soldiers or clergy being moved from one post to another


• boatmen or coach drivers who operate the means of transportation


• messengers/couriers traveling from the major portal cities throughout the surrounding territories


• traveling performers, circuses, etc, who make their living on the road


• merchants transporting goods from one market to another

In almost every case, it seems like the standard routes would exhibit hub-and-spoke patterns. You'd go to or from the nearest portal, but rarely go through. And given that there's only one portal per continent, they'd probably be multi-leg journeys. So maybe only one of ten boatmen or dogsled-drivers or whatever would actually be the one who saw the city on the last leg of the journey. The exceptions might be clergy being assigned to new parishes on other continents, since as you say the religion is worldwide. Soldiers likely wouldn't pass through the portals in peacetime.

Even merchants if they went through would not go very far. The portal cities are the obvious places for trade between different nations/climates/etc, so while a merchant may go through a portal to another part of the megalopolis, he's not likely to then go jaunting off into the countryside of the foreign land. And even given such exceptions, merchants and troubadours and clergy make up a pretty small slice of the population. They are specialists with special reasons to use the portal, reasons that others don't have.

For most people, portal travel might be a one-time event

In addition to a few specialized professions who regularly travel to the portal cities, there are a number of reasons why a medieval person might travel to, or through, the portal city once or twice in a lifetime:

• as pilgrims on a journey to a holy site (or the return trip)


• as warriors on a crusade (or the return trip)


• as refugees fleeing war or natural disaster


• as explorers or settlers emigrating for better opportunities in new lands

This still leaves the bulk of all living people as non-portal travelers

Most people probably live hundreds or thousands of miles from a portal, and given the era, may never in their lives travel that far. I would guess that people who live in or near the portal cities might go just for sightseeing, but people who live farther away would only know about the portal cities through tales told by sailors and pilgrims. Many routes between major (non-portal) cities on the continents might not even pass near the portals.

The relevance of portals depends on (un)lucky geography

Following on that thought: population density on most continents is probably like in our world: most people will live in fertile river valleys and along the sea coast where the climate is suitable for farming and the waterways are suitable for trading. Since there's only one portal per continent, if the portals are distributed randomly, many may be found in deserts, mountain ranges, or plateaus far from major waterways. On those continents, it'll be very hard (and expensive) to get to and from the portal city, so those portals will be relatively little-used, and life will go on relatively independent of the other continents. Only on continents where a portal is lucky enough to fall on a fertile river delta or near a sheltered deepwater port will the portal really play a major role in the economy and politics.

Using a portal has unpleasant consequences.

Other people have already covered the "what if it hurts you somehow" angle. They've missed a trick though which anyone familiar with Warhammer 40,000 should know.

How are the portals powered? Answer: by sacrifices. The psychic energy of their deaths provides the necessary power source to transport a payload through the portal. (Bonus points if the sacrifices are human. Extra bonus points if they're children.) The more you transport, the more sacrifices you need.

The church of course says that keeping the portals running is a holy work. The sacrifices go to their end secure in the knowledge that God will bless their souls in the afterlife.

And yet... Some rational people oppose the church and the human cost of running the portals. Publicly voicing their opposition would get them executed, of course, but they can at least be sure that they themselves have not caused the death of another person by using a portal.

For extra extra bonus points, perhaps there is even a good reason to need the portals. In the Warhammer 40,000 universe, of course, the Emperor of Mankind defends humanity to keep the species alive; and psychic humans who are too weak to resist demonic possession are a major threat anyway; so sacrificing them to the Emperor by the billion serves a dual purpose in keeping humanity safe. But the psykers are still dead.