Discussing this topic one has to think about the following:
The rules in Traveller are written for player characters and therefore for a small niche in the interstellar economy. But those rules are meant for the smaller fraction of the economy and not the big part. Simulating an economy might be a bit much for a few pages. So we should not assume the whole economy works as written in the rules.
Big corporations will have more ways to make a profit. They might get the ship cheaper (or might have built it in one of their own docks for a much lower price), get the nice contracts and might be able to charge more. You could ship your valuable possessions through pirate infested territory using this flimsy Free Trader over there. Or you could use the big, escorted transport of a mega corp.
To be an alternative the Free Trader has to be the only or best option. Therefore you need to be cheap.
Long-term contracts are another thing that aren't represented by the rules, because doing the same thing for years might get really dull.
The other part about shipping cheap goods with expensive ships: What's the alternative? Skyrocketing the prices of simple goods could completely destroy interstellar trade or even whole worlds.
