Kyle A Flying Pokemon can fly without knowing Fly; it's one of their natural traits. However, it needs to know Fly to use the attack and to be able to transport people that way.

You keep on moving. Aerodactyl yells down that a few Taillow are flying up near him. You also notice an Oddish who has planted itself in the ground, and you avoid stepping on it. A sharp buzzing alerts you to a Scyther flying low to the ground, seemingly ignoring you. What do you do?