As the Rebellion starts commercial shipping is a big target of commerce raiding by opposed factions. In response the megacorporations cut down the frequency of their trade runs and move the majority of their assets away from contested borders and systems. Thus the reliable Imperium-wide system of trade has broken down, but people still have goods (including themselves) that they want to get from one place to another, and if the major corporate liners and freighters aren't making the runs anymore (or are making them so infrequently that the shippers can't want -- or demand for the limited space is so great that they can't afford the price) then they're going to turn to the independent operators, the small PC run vessels (the same way that the market in black-market unlicensed taxi services has exploded in LA during the transit strikes of the last few weeks). As long as the PCs are willing to go where the big boys won't and aren't afraid of taking a few risks they should be able to rake in cargoes, passengers and credits hand over fist. However, the situation is far from stable, and as the Rebellion drags on people will become decidely less interested in traveling and shipping goods across borders. Trade will shrink and become concentrated in the faction safe-zones, where the big-boy megacorporate lines are still in operation. And then the PCs will be back where they started, scrambling like mad to keep the cargo holds filled and make enough credits to keep the ship running -- only now the pressures aren't coming from the bank and the megacorps, they're coming from pirates and black-war fleets and the lack of shipyards capable of performing a proper overhaul.
The trade system in the rulebook (which is IIRC identical to that from CT Book 7) probably doesn't reflect the above situation, but that's where referee fiat comes in.
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