It sounds like you're just imagining flyers on another 2-dimensional plane above the one on the ground, which is not realistic. If they can fly, they can be just as far from another flyer as they can be from a guy on the ground. They're not just standing on the roof, they can be above and below each other as well.
If they don't want to be close to a guy on the ground, why would they want to be close to a guy in the air? Either they're wanting to be distant, or not.
Regardless, the mechanical rules are quite clear that flyers can shoot each other with ranged attacks. If you don't like the thematic justification that I use, you are free to invent your own, but that is the way it works.
Edit: The hinderance statement is a good point though. I'm not completely certain how to justify two creatures being far enough to shoot each other yet still creating hinderance for one another.