The ability to use (and not use) flying mounts in the leveling experience in Mists has been a ... topic of some debate amongst people. Some feel it's added the overall experience, while others are upset they don't have the ability to dive out of the sky anymore and quest super quickly.
Blizzard was pretty adamant that this design decision was necessary, and Bashiok indicates in his post that's how they still feel.
More importantly, however, is that Bashiok notes there will be no flying in the new zone coming in patch 5.2. It'll be very Isle of Quel'Danas-like, for those of you who've played there during The Burning Crusade
Bashiok's full statement is as follows (bold added for emphasis):
We pretty firmly believe the questing experience is just wholly better when you can't lift off and set down wherever you like, frog leaping from quest objective to quest objective. Certainly we've supported that with no flying for the leveling content of Wrath and Mists, and only after you hit level cap can you obtain the ability to fly. The new zone coming in 5.2 is not unlike the Isle of Quel'Danas in a few ways, and one of them is that there's no flying.
That helps us achieve that desire for progressive questing, it's good for supporting world PvP, as well as lets us make really difficult outdoor encounters, like Oondasta - who is OG Kazzak in difficulty - that you can't just drop on top of from the sky.
I can't imagine flying mounts ever going away, they're a big part of the game at this point, but certainly they can take a break when it makes sense and we can present content in a more intimate way from time to time.