Flying is completely asymmetrical.
Because a flying creature can move in 3D, they have literally infinitely more options for movement and positioning than do grounded creatures. There is absolutely no response to it for most creatures.
Ranged attackers tend to do OK, obviously, and of course anyone else with flight is fine, but melee, grounded creatures are usually out of luck. A back-up ranged weapon is rarely sufficient to actually threaten flying creatures, as generally one will not have the feats or class features to support it, and there isn’t really any other way to deal with the situation.
This is just a fact of the game system. Once flight becomes available, it becomes imperative that everyone gets flight ASAP. It’s often cited as a major reason why the weaker classes are weaker.
As the DM, your only real options are: design every encounter with ways of responding to flight, or make sure all meaningful combats take place in an enclosed space that prevents flying. Both of these are extremely limiting, unfortunately, but they are the only real ways to deal with it.
Or, you start houseruling things. My personal choice is my abstract flight variant (technically it’s for 3.5, which means there are no references to the flight skill, but adapting for Pathfinder is fairly simple) – it makes flight fairly unrealistic, and accepts occasional breaking of verisimilitude/immersion, but it’s massively simpler to run and makes flight not quite so one-sided.