Are these problems that you've run across?
I've been avoiding combat like the plague after some initial poking around, so I can't say too much about it (but sometimes it finds you and you just have to bite the bullet). The way it works, far as I can tell, is that you really shouldn't just go and pick random fights hoping for kewl lootz. The generic loot from some raiders or undead is going to be meh, and is unlikely to offset the cost in supplies and rehiring of lost crew. Taking a well-paid mission, or following on some story bits should nett better results. Rare non-cargo curios, like jewellery etc., don't take up space and can bring some good coin.
If you know what you're doing, and why you're doing it - it should work. But I don't think you'll ever be overpowered enough just go looking for trouble.
As for the general economy balance - it's tight, but not unfairly so. I'm on my first run, other than early tutorialising, and I'm seeing a steady influx of cash doing mostly just trading/cargo missions.
It's much like Sunless Sea/Skies, down to literally the same type of complaints you hear. If you're familiar with those games, the way to make money is by combining as many ways to make profit on a given route as you can.
Take any ferrying missions, buy some stock you know is in demand along the way, maybe consider taking passengers if they're going in the same direction. As long as you take care to exploit all available opportunities, you should be fine. What bleeds money is empty runs, buying random cargo and hoping it'll sell, and overhiring (caravans can be easily downsized and later upsized again, at a rather modest loss).
Unlike the Sunless games, there's a sensible save system, so you never lose everything to a single bad decision and can experiment with what works or doesn't, more easily.