My Illogical Theory
Because most of them are birds. And, birds are pretty Normal.
Like, excluding the ones like Butterfree and Gyarados, who have an obvious, needed second type, the Normal/Flying Pokemon are mostly birds.
Except for some other Pokemon like Swablu, who really is a bird, but I think could be based a normal cloud, and Togetic and Togekiss, who might get it's type from it's prevolution Togepi - but otherwise, except for the Fairy-type, which it later got, what type could it have?
Also, Flying is a very obscure type. Like, a Rock-type could just be a Rock like Geodude, A plain Ghost-type would be a ghost like Misdreavus, a Dark-type could just be a Dark Pokemon like Umbreon, a plain Dragon-type would be a dragon like Dragonite - what would a Flying-type be? Something with wings? Say that to Gyarados or Tornadus.
So yeah, that's pretty much the reason. Almost all Flying-types are birds, and therefore get that added Flying-type.
Hope I helped. :)