It's a problem mostly if you as a DM aren't ready for it.
Some considerations:
a) Winged flight (which is not stable and requires a lot of space) is not as problematic as magical flight (which is stable and generally only requires the sames space as a body).
b) Low maneuverability flight is not as problematic as high maneuverability flight that allows hovering and other maneuvers.
c) Flight available to one party member is not as problematic as flight available to all party members.
d) Flight available at will is less problematic than flight available for short durations.
e) Beware rule sets that simplify all flight to its least problematic sort. A more complex rule set that limits how you can fly and what you can do while flying, at least for anything short of a flying carpet can let you introduce flying more easily.
f) Beware rule sets that reduce all the risk of flight. Flight ought to come with inherent challenges related to the fact that you are moving at a high rate of speed at height. Flight is dangerous. Losing flight ability while you are 100' off the ground is or ought to be a problem.
g) Be aware that by some tier, flight will be available and will be increasingly available at higher tiers. Prepare and plan accordingly. In particular, most encounters should involve foes with ranged attacks, or which can fly, or in enclosed spaces where foe is maneuverable enough to dominate the space. And if on occasion they do kite a less maneuverable foe, don't get upset about it. Congratulate them on their tactical acumen and success and move on. One of the worst impulses that can inflict a GM in my opinion is the need to impress players with their encounters, and fantasies about how successful your monsters or traps are going to be are to be avoided.
h) Be aware that your society is one that has experienced flight being available to some extent and will have planned accordingly. In a world of fey flying boys, upstairs windows will in fact be shut and barred at night, for example. Parapets will be routinely built with enclosing hoardings, and not just as an emergency measure when preparing for a siege. And so forth. Society ought not be surprised by low level flying magic.
You'll note that rule sets like 3.5 tended to multiply the problems attendant with flying PCs and from an earlier point. For example, one of the earliest forms of flying available was fast, magical, stable, highly maneuverable, had a usefully long duration, and had a built in magical safety device that floated the character gently to the ground if the spell's duration suddenly ended. I put it too you that fast, magical, stable, highly maneuverable flight, with a usefully long duration, and a magical parachute built in is useful enough that if it was a higher level spell than 3rd, casters would still take it. Further, I note that that is a huge jump in usability compared to Levitation at 2nd level. So in short, if you are worried about the impact of flight on your game there are ways to make flight useful without making it game breaking.
To a certain extent I like having some amount of flight available in that it becomes a useful problem solving resource. There is always someone in the party who is about as agile as a rock, and while you can punish that with scenario design what you don't want to do is punish that so severely that certain scenarios are effectively dead ends because part or all of the party can't overcome the obstacle. Having someone able to play taxi for the less mobile characters is more useful to the DM really than it is to the party.