Indeed, most things in Pkmn such as how Bayleef can shoot out so many leaves, etc. are meant ta be magical abilities, tch, but then there's geeks like me who always try ta find an explanation ta everything. XD
Oay,here goes: I think Rayquaza's got certain chemical and physical processes goin' on inside tha cells in either her whole body, tch, or only in speciallized cells found in tha scales(I'd say tha whole body) that produce a kind of electromagnetism that either repels or nullifies the earth's own, and by varying the amount of magnetic Charge in different parts of her body she can propel herself through the air.
Kinda like a bit stolen from Beldum's PokeDex data I know, tch, but that's how I think she does it.