Per Liath's comment, it would depend on whether or not these flying beings have legs/are capable of walking, or if the only appendages they have are wings, and/or their body structure in general.
If it is the former and assuming that their physiology is similar to Earth's birds, I believe that it may be likely that they would develop the wheel eventually. Constant flying (near 24/7) would be awfully tiring, and we do see flight-capable birds on the ground and wandering around.
Goodness knows I've seen some that decide to slowly walk across the road where there's a lot of cars and they're at high risk of being run over - and I'm always thinking, 'you have wings! Why don't you just fly across the road?! Surely it'd be safer/easier!' but seeing as they don't and decide to leisurely make their way across... my guess is that they're resting their wings. It doesn't seem to make much sense otherwise.
So, if these beings are also capable of spending some time on the ground (or a flat surface of some description), then yes, I do believe it's likely. If say, however, their society is based in the trees or something, which they hop or fly around to, and there aren't any sort of "platforms", or walkways between them, then a wheel would be next to useless for them. Wheels are used for transporting things from point A to point B, but if the path between point A and B aren't suitable (don't cater) to the usage of wheels...
TL;DR:
###TL;DR:### ItIt would depend on their A. physiology, and B. societal infrastructure.
[EDIT] And after reading some of the other answers and thinking about it some more... No one society exists in a vacuum indefinitely - sooner or later, they'll discover another completely different one. So another thing to ponder would be, would there only be just the one society of flying beings on that planet? I mean, other nearby societies may be ground-based. Assuming that some form of trade may one day occur between this flight-based society and other non-flight-based societies... sooner or later, someone's going to invent the wheel, would be my guess.