Well, there is no absolute answer (except for the taboo "because GameFreak wanted it that way") but here is my theory.
Garchomp's deisgn looks aerodynamic, but it has no way of flying high into the air, which is required to use Fly. I think that the pokedex entries simply means it can move very fast, maybe even just off the ground, but it can't get the lift required for true flight.
Also, notice that it does get Aerial Ace (a lot of non-Flying Pokemon do, though). Aerial Ace is different as (I imagine) it can be performed by a Pokemon that can jump well.