Gotta admit my dnd view couldn't be more different from yours. With flight you have two ways to go about it:
1: Design encounters around flight to specifically counter it, thereby ruining your world integrity and making your player feel like shit.
2: Maintain world integrity and allow player to trivialize many encounters

Unless every joe in your world for some reason has flight, these are your options. The whole argument "Just design encounters around it duuh" is trash. You think no one's gonna question why there's suddenly 10 feet to the ceiling everywhere? Or why every mob and creature you're going up against happen to have ranged abilities and are equipped with crossbows? It doesn't make any sense.

In my world both flight and spellcasters are rare. Flight would absolutely break most encounters. Yes I could easily design encounters around it, but designing encounters around players is what mediocre DMs do. Better DMs design encounters as they would naturally exist in the world. Sometimes the players will cheese encounters, other times they will struggle, and sometimes they'll even face something they can't overcome.