Ports are too expensive to travel on.
Right now Ports charge way too much to travel with, even without taxes. A warrior in plate armor usually costs around 200-300 gold depending on what he is carrying. I shudder to think how much a fully loaded cart costs to ship across the sea. Right now we need a reduction of price, probably by half or even more. Its a bigger problem of traveling between cities take too long, but better ports may mitigate that issue.
You may have missed the info regarding ports, but they are not designed to be used as casual travel. They said the ports are meant to be that expensive, and used only for emergencies. Not as an easy travel between parts of the map. I actually thought they were cheaper than I expected when they said this.
What emergencies? Right now players rarely carry gold (instead depositing into their cities) and if saying PVPers were beseiging a city they would need about 10-20 mins of grinding to use it. I suppose people could carry the gold with them but everyone wants to buy a resource without traveling to the location by depositing to the trading post or buying resources.
Right now most players refuse to trade with each other because traveling and trading could take HOURS to complete. Ports were realistically centers of trade and shipping but right now its barely being used.
I get ya, and actually agree with ya, but that's what they said. Basically "hunting monsters and trading is meant to travel with horses". Check out the Fall Alpha Dev Update #1 video, about 9 minutes in.
Ports in this game are NOT meant to be centers of trade, per se.
They put ports in as a way to travel from one side of a continent to another, in case say your Guild is getting ready to do a raid and you happen to be on the wrong side of the map at the time the raid is going. Of course, Legends haven't really spawned as of yet, so Raids are a future thing at best.
Ports are NOT allowing Carts or Wagons, so to answer your fears, no worries, you don't have to come up with thousands to move your cart/wagon via ports, as you can't do it at all.
The game is meant to not have fast travel in the general sense of it. The only time a port would be usable to carry goods above your character and what he/she is wearing/has in their backpack is when new continents are implemented. I believe then, they will have only very specific routes that can allow that kind of stuff to be transported.
As you say, PCs don't carry gold around with them if they can help it, so what you're going to want to do, if using ports is something you think your going to do with any frequency, is to specifically store some gold in the Banks of the Port towns your most likely to use, that you can draw upon in those times of emergency when you gotta use the ports to get to a guild raid, or help a friend on a corpse retrieval, or something of that nature. It's the same kind of forethought that will have a lot of PCs keeping a spare set of workable gear set up in commonly used town banks in case they die and need to do a corpse run from those locations.
Also, food for thought: Right now, there really isn't any Gold-Sinks in the game. Towns have upkeep, and private individuals not in towns can buy exactly 1 house, and after that, there's nothing for an individual to really spend Gold on at the moment, so stockpiling gold for Port fees is at least something productive you can do with the nearly useless commodity. Later, when Gold gains a real sense of value, things may be different, but right now, dropping 200-300 on a Cross-continental trip is actually a steal.
I don't think 200-300gp is that bad to be honest.
If you are a merchant and on the other side of the world ores 50 gold coins cheaper, 300 gold is nothing.
Usually traders only travel the cities on horseback and build a cart if necessary and then buy the goods.
And you have to keep in mind that port cities have to generate so much revenue that they can compensate for an ore mine because they have no other resources.