You can always not fly if you want. /shrug

But I don't really think it's a problem, especially with the way flying works in this game (as compared to something like WoW pre-WoD). You have to do the MSQ for each zone and explore them all before being able to fly in them, so it's not as if you can just grab the flying ability and breeze through all the zones right away. The only real benefit to flying in this game is being able to reach HW hunts and side-quests faster. And maybe future main story quests.