Mew, Vibrava, Flygon, Lati@s, Giratina(Both forms), Arceus(Who can be a flying type), Golurk, Hydregion, Volcarona, Reshiram, Zekrom, Kyurem, and Genesect. As you can see most have been shown as flying and many have the ability Levitate.
Trivia: Charizard could not learn fly in Red or Blue but he could in Yellow. There are no non-flying types in Johto that can learn Fly. Most non-flying types that learn fly are Dragon types, even Arceus can be one.
Those are the ones that can learn the HM fly.
Pokemon that are not flying types that fly anyway.
Geodude, Venomoth, Weepinbell, Victreebell, Magnezone family, Gengar family, Wheezing family, Mew, Porygon-Z family, Mismagius family, Scizor, Celebi, Dustox, Shedinja, Meditite, Volbeat, Illumise, Vibrava, Flygon, Claydol family, Castform, Shuppet, Duskull, Chimecho, Beldum Family, Lati@s, Jirachi, Bronzong family, Spiritomb, Garchomp, Carnivine, Dusknoir, Probopass, Frosslass, Rotom, Uxie, Mesprite, Azelf, Dialga, Palkia, Giratina(Origin), Cresselia, Darkrai, Arceus, Victini, Musharna family, Whimsicott family, Cofargius, Family, Reuniculus, Vanniluxe family, Klinklang family, Beheeyem family, Lampent, Chandelure, Crygonal, Druddigon, Golurk, Hydregion, Volcarona, Reshiram, Zekrom, Kyurem, and possibly Genesect(Nothing is confirmed yet).