A lot of how good flight is depends on the adventure. I think we can all agree on this. Traps, natural physical obstacles like canyons, fighting creatures without range, navigating labyrinths, etc. Flight is god like. Here is an example:
The adventure consists of one RP, two skill challenges and two combats. The RP is to get past the bouncer and go upstairs to talk to the eccentric artist that is high all the time. He has a map you need. Technically, flight could just take you to the upstairs window. Next, you are traversing a maze of canyons. Oh, flight just took care of those navigation rolls. Oh no, there are giant scorpions in these canyons. No biggie. I fly up, and just shoot arrows or cantrips at them. Hey, we just came to a place where a climber needs to cross a dangerous and sharped rock wall. Flyboy - I got this. Reach the end, a giant twisted malformed willow tree, here in the desert. He is using all the water and killing anything that gets near his pool. Again, I fly and stay out of harms way while shooting arrows or casting spells.
Note: I am not saying it would be like this all the time. But there are several adventure types that flying can come across as a super power. A campaign on a ship is another one. In the end, it just becomes a thing the DM accounts for and builds things that work against it. In the ship example, there is always strong winds or storms or archers or giant flying wasps or whatever. Then, the danger is, it becomes a game of tit-for-tat. And that doesn't make anyone happy.