So, let's say someone were hypothetically putting together a setting minibook, and one of the options they were exploring was a fairy race. How disruptive would you consider it to have a flying race as a basic option?
It depends on the whole package. The race builder will give you a rough idea how your race compares to other races.
You especially need to look at low-level play. By 5th level other characters are starting to fly as well. In the mid-teens you can get the whole party airborne easily if you care to.
I would limit speed or maneuverability as a racial feature or give them a significant disadvantage. I also suggest having feats to allow them better flight later on if they so choose.
In low-level play, you need to worry about avoiding challenges, and ranged attacks.
Flight makes some dangers nonexistent to the character. Pressure-plate and pit traps. Pools of water or acid. McGuffins that are placed high. The flyer can simply avoid these.
Flight also makes challenges with melee attackers easy. If they don't have ranged options, the flyer can circle above and pepper them with ranged attacks. Even acid splash works wonders when the opponent can't target you.
It gives pretty huge advantages up to about level 4 or so. Starting at 5 other casters get flight so at that point not as big of a deal.
For the one homebrew race I did, I tried fitting flight in early and it caused issues. Eventually I settled on the race had lost some of its power but with effort could be reclaimed. Basically their wings grant feather fall and the ability to glide early on (pretty cool), but they can take a special racial feat at level 5 that grants them their normal flight speed. Seems to work pretty well so far. Another feat higher up (9th I believe) lets them increase their fly speed and ignore armor effects on it.