Faolyn
(she/her)
Well, why not include flying or ranged attacks into every combat? As I said, there's no reason why your humanoid foes shouldn't have ranged attacks. And if you have a lot of PCs flying around, they're going to attract attention from other flying creatures. Unless your player is specifically playing a flying creature in order to be invincible, then they're going to expect to be attacked. And if they're playing a flying creature specifically to be invincible, they're munchkinning/power gaming/whatevering and you can target them with impunity.Because unless a DM forces in flying and/or ranged attacks into every combat, the second one starts with just melee monsters (which is a good portion of the MM, and includes a lot of animals and things that many DMs would consider standard fare in outdoor encounters), then the flying PC is invincible.
Also, while flying, they're not going to be able to Help their allies, provide flanking bonuses, take advantage of cover, or do any of the other things that grounded PCs can do.
But here's another thing: going by RAW (IIRC, at least), you can move then attack, attack then move, move then attack then move some more, but only specific maneuvers and (maybe) feats let you attack while moving.
None of the flying heritages, to my knowledge, can hover. And while the rules don't call this out specifically, I'd say that means they are always moving while flying. So at the least, if they want to stay up in the air and pepper their opponents with their own ranged attacks and spells, it's completely logical to have them roll with some sort of penalty.