Too few (good) moves, too many common weaknesses, eats up a mega slot where a Terrakion could have been. Also mentality. Originally, Aerodactyl had the niche of Sky Drop, but when that trend dropped so did the 'mon's usage. Like many other pokemon, it has potential but not enough to satisfy the general public (or the metagame at times).
People do use Mega Aerodactyl btw :o, from what I've seen it's about as common as a Latios (that's rare xD, but there alright)