Why and How, indeed.
This is where we actually disagree. I have stated that for some campaigns, your "how" to deal with it might lead the player to think it is a game of tit-for-tat where they feel targeted. This is especially true if only one PC is able to fly. That is why I gave the examples. But, let me try one more time.
Party of four. One flying. Searching for some lost tomb in the desert.
- Scene 1: Navigation of desert terrain to find the canyon that the tomb is in. Much easier with a flyer.
- Scene 2: Bizarre sand trolls that hunt from on top of the chasm. They toss big rocks down. That's how they kill their food. Pretty easy for a flyer to stay above them.
- Scene 3: Crazy sand worm or scorpions that burrow into the sand and pop out. Flyer stays out of range.
- Scene 4: A steep canyon wall climb to get to the hidden door. Flyer does it no problem.
- Scene 5: Small cave entrance with an iron door. Party huddled inside the door which is trapped. The flyer is just hanging outside the cave.
- Scene 6: Inside finally. The flyer's potential in an Egyptian style tomb is negated for the next four or five scenes.
So the flyer can dismiss half of them. That is a lot. Now, of course any DM can make sure there are stirges next to the scorpions, and the trolls have small rocks too (for whatever reason), and there is always a sandstorm in the distant that makes navigation by air impossible, and the door explodes with gas that just happens to reach the flyer. But, if a DM did do all of that, the flyer might feel targeted.
I don't know. This is just a quick example. But, it demonstrates my point. The "how" a DM handles the flyer, even when doing it right, might still come out as negatively perceived.