To me the issue is that standard scenarios that I’d expect to happen in a fantasy story don’t work if a PC has flight. Heck, a bunch of published adventures don’t work if a PC has flight.
-The players need to go through a dark forest filled with dangerous wolves.
-The players need to climb a mountain in order to find an item at the top. It’ll take 2 days to get to the top because going straight up isn’t an option. Over those days they’ll be attacked by polar bears and yeti since they’ll have to pass by their lairs.
-The players need to find their way down a trap filled hallway, where touching the ground is dangerous.
-The players come to a chasm where the bridge is out and are forced to take a detour around forcing them to spend the night in a nearby haunted town.
-The players need to transport an unconscious guy with an anti magic aura on him to the one place that will be able to heal him but there are demons (without flight) waiting to ambush them on the road there.
You seem to be assuming that every player in the party will have flying abilities. How often has that actually happened? Most likely, you only have one flying PC,
maybe two, assuming you have any at all--there are a ton of heritages out there, and only a tiny fraction of them have any access to flying abilities.
What that means is that all of these problems are only going to be bypassed by one PC and the rest have to go through. The flying PC can't carry everyone past the challenges. If the rest of the players are
angry that this one player keeps bypassing the challenges, then it's a problem in the party. Otherwise, it's just the Narrator being annoyed that their plot didn't go the way it was supposed to go.
So let's look at these challenges here. Wolves, polar bears, and yetis? Add giant spiders (ranged attack), or griffons or wyrmling dragons (flight).
Trap filled hallway? Is it wide enough for their wings? Even with the most generous and magical of estimates, a Medium PC should have a wingspan of 10 feet at minimum, so if the corridor is 5 or 10 feet, it's not going to be wide enough. Is the ceiling high enough for them to fly? Probably not; a 10-foot high ceiling isn't going to be enough for a character that can't hover. At best, they would need a series of Acrobatics checks just to make sure they don't crash into the ceiling or walls (and feel free to trap them as well!) or into the ground. Flight's not going to be a help here.
A bridge is out? What would you have done if the PCs decided to climb down the chasm, fix the bridge, detour in the other direction, or take one look at the town and nope their way to a non-haunted campground? I assume you weren't going to railroad them to the haunted town and wanted them to get there naturally, but there's a
lot of ways that encounter could go that doesn't according to plan.
Anti-magic aura guy? Too heavy to carry for long. Or his anti-magic aura interferes with the character's magical flight (if applicable). Or his wounds or illness is such that he can't be jostled too much, so flying him is too risky and he needs to stay in the cart. Or, again, give the demons, or even just
one demon, flight or ranged attacks.
These are just a few of the scenarios that have actually come up during games that would have been ruined by one person having at will flight. There are countless more. Does each of these have a “solution”? Sure. But do most of those solutions either feel like you are purposely taking away a player’s ability or feel very contrived and artificial and possibly a little unfair? You bet.
Not at all. Again, your players should expect to be challenged. It's not singling them out take that into consideration when you design your encounters. It's only singling them out if you
never let their flight actually be useful, or use ridiculous methods to nerf it.