From a pure odds standpoint, you're more likely to beat the other guy's trips (assuming that's what he has) by drawing for the flush than drawing for trips. You have about a 19% chance of catching the flush on a 1-card draw and more like a 13% chance of getting trips on a 3-card draw.
Also, if he's a smart player who pays attention to your draws, he'll assume you're either going for a flush or straight by drawing 1, and it will be easier to bluff him off trips if you don't hit. If he's not, or if he tends to call down with a decent hand, you'll probably want to check/fold if you miss the flush.