I hear you, and you are correct. But you are leaving out the mix of encounters, and that's where it becomes tit-for-tat.
If you have a party travelling by air, sure they encounter flying things. You build encounters around that. You have sea encounters on the water. But when you have one that can fly and the others can't, constantly throwing a wrench at the single flying party member so they too have an encounter looks like tit-for-tat. It does not look like a natural encounter.
Here are some examples:
- A party travelling encounters a gelatinous cube in the swamp. Now, in order to make it fair, there just happens to be a tree full of stirges as well. The stirges just happen to be at the same location.
- A party travelling through a desert encounters a sand golem. Now, in order to make it fair, the sand golem is modified and able to throw sand-hands or something just as silly at the flying PC.
- The party travelling across a fjord are ambushed by a sahuagin patrol. Now, in order to make it fair, there just happens to be a priest with them, so they have a range over 60'.
- The party travelling through the forest comes across jackalweres. Now, in order to make it fair, the DM extends the jackalware's sleep gaze to 60 or 100 feet.
- The party travelling through a huge, high cavern of some ancient race comes across a large group of grimlocks. Now, in order to make it fair, the cavern ceiling is lowered to 8' so the grimlocks can actually hit the flying PC.
Again, I am not saying it destroys the game or creates a giant imbalance. But all of these examples, which are
level one encounters, now look as though they are built for one player, and one player only. As opposed to being more organic or natural. That has a tendency to make the player wish they never would have taken flying in the first place. You could create the same examples for skill checks, traps, and navigation.