That's essentially what I've done IMTU. Actually, I don't use any of the starship economics rules any longer. I simply assume that - unless a particular adventure plot requires it - the income from each routine/legal trading journey just about covers the ship's standard expenses (fuel, berthing, routine maintenance, monthly loan payment, salaries for NPC crew, etc) and nothing more. 

In-game, I think this models rather well how tramp freighters operate on the knife edge of disaster, with any major unexpected expense normally being enough to drive the owners into bankruptcy or criminality. Out of game, it means that if the party wants to make a tangible profit, then they need to find themselves an adventure . . .