My Velocity has flush caps.
Cessna used to have a type of flush fuel cap. The eventually became known as the "killer caps" as they could allow water in. So I'm guessing that potential to allow water in is the reason you don't see flush caps on GA aircraft.
There was an AD against those caps:
http://www.airweb.faa.gov/Regulator...7CA32CBFD7107A87862569B9004D1566?OpenDocument
And that wasn't the first AD. An earlier version regarding leaking caps applied to the 182 only. That one, 83-13-01, warned of loss of fuel and erroneous fuel gauge indications if the caps leaked badly enough. The low pressure atop the wing would suck the fuel out by removing the air from the tank faster than the underwing vent could replace it, and the bladder would collapse and lift all the fuel and squeeze it out past the cap's leaks. The collapsed bladder would hold the fuel sender float up, giving the pilot the wrong info about fuel in that tank.
And even then the ADs weren't detailed enough. They mention checking the cap seal, which is a large-diameter o-ring, easily seen, but neglect to remind us of the little, hidden seal around the locking shaft. Either of those seals are happy to let water into the tank if they're old, shrunken, or cracked. Being out in the weather like they are, they don't last that long.
Terminating the AD meant replacing the flush caps and their filler necks with an adapter to the smaller filler neck and raised caps with the big rubber gasket we're familiar with. Still not perfect, but better. The best systems I've seen use a sealed, hinged cover over the cap, and a drain from that cavity carries away any water that gets past the cover before it can find its way past the cap.