Unlike Spring Attack, Fly-by attack does not have an effect on AoOs. The AoO is provoked as normal. If the flying creature has Spring Attack instead (or in addion) to Fly-by Attack, there is no AoO.
A quick note: Fly-by attack allows you to place a standard action inside of your movement action. It does not require that standard action to be an attack. The creature could use a spell-like ability, cast a spell, sunder an item, use an item, etc ...
A personal favorite tactic of mine is to have dragons use fly-by attacks to fly out of their lair, breath and then return to safety, usually in another cavern. Sure, PCs can launch a few readied attacks at them, but they usually can't take the dragon out and the dragon can restore itself once in a safe location.