There is a significant difference in danger between being semi-afk when flying and when using a ground mount. Mostly by virtue of the paths you need to follow to avoid enemies are fairly narrow and often winding in weird directions, when flying the only risk you are running is hitting a mountain to trigger normal ground mount mode, or overshooting and hitting hte fatigue zone.
But yes, there is definitely a way to make flying dangerous enough to force people to the ground, but i am, not sure it would work regardless.
I have yet to see a zone in WoW trily made better by the inclusion of flying mounts. Even zones thyat require it often make me consider how it could be made more epic by removing flying entirely.
The airships in Icecrown are cool and all, but what would make it really interesting as a gameplay element was if it allowed you to parachute down, meaning the meandering movement across the glacier would serve a gameplay purpose.
Storm peaks as well, cool as it is to create a zone that requires flying to navigate, it also lessens the size and spectacle of the areas around you as flying to the top and noticing how small the area really is lessens the illusion.
The new zones in Cata are perhaps closest, but even then mostly because many of the questlines ground you or otherwise removes your flying entirely, Hyjal for instance loses some of the intended effect of descending the mountain as flying makes backtracking to higher areas a simple matter. Vashj'ir is perhaps the only zone to truly make "flying" feel integrated into the game, and players hated that zone.