Ignore the mortgage.
Calculate the costs involved for fuel, life support, annual maintenance payments, crew salaries.
Now how big is your cargo hold? You set the price to pay to ship freight from your per jump costs. Your competitors will have to match this. If you want to drive out your competition you can subsidise your freight costs from the profits made by selling the goods,
That is what it costs to transport goods for the megacorporations or a government - the megacorp will pay for ship construction from profits, while a government can use general taxation. They make profits from the goods they transport, not the freight, so if you want to compete in the freight haulage business you have had it if you have a mortgage to pay as well.
...
That's most of it.
As I observed above, the capital and operating costs of the most efficient available ship will set the floor for shipping costs. However, this is the floor, not the ceiling.
A given world might not generate enough cargo to fill the most efficient available ship on a weekly basis. So it won't visit that often, and you might find someone willing to pay more to ship now than wait for the next big freighter to come through.
There might be pirates, or a war, or political issues (or, heck, Negative Space Wedgies) that make interstellar commerce less than perfectly safe in the area. Megacorps' insurers might balk, but a daring PC crew might be willing to take their chances and harvest the risk premium themselves.
There might be a high-Jn milk run that the local tech can't build a ship for -- at least not profitably. Come in from a couple of dozen parsecs away with your TL-14 or -15 wondership and you can clean up until someone else notices.
And coming at it from the other side, there's the question of how profitable the cargo can be. At some point, the costs of shipping will exceed the potential profit from selling it, at which point there won't be any demand for shipping (on that route).
That said, in general the higher-Jn ships will most likely be built for, and stay on, routes that use their range to its maximum capability. For game purposes, they'd be settings rather than PC-owned ships since they won't be wandering willy-nilly across the sector; instead, they'd just go back and forth.