If I think about it I'm sure they're super prevalent in, say, steampunk or something (?), but I don't read/play/watch anything like that so Final Fantasy is the only thing I can think of when i think airship. But I think you'd be more hard-pressed to find a fantasy rpg that doesn't feature some form of white/black mage that casts fire/thunder/ice/cure/revive than you would be to find a game that features airships.
EDIT: I thought of one! Bioshock: Infinite! Pretty sure the whole game was set on airships.