I just equate it to the fact that Bugs in the real world aren't generally built to sustain flight for a carrier. It's silly in a fictional game like Pokemon, but that's the only thing I can hinge on. I had to look up Fly to see what Bug-types could learn it and none apparently do. So rather than being an oversight, it could be a conscious decision not to have them learn it.
Again, it's weird when you figure in the games a Pokemon like Yanmega could probably EAT a damn Pidgey, so why does the tiny bird get to Fly and ferry people across the skies while Bugzilla can't? I throw my arms up to the question.