There are a variety of reasons for why it may be more desirable to travel by ship or caravan.
- Lack of faith
- Desire for adventure
- Unwillingness to leave their life in "God's Hands" regardless of faith
- 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.
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.