We built some games in Flash/Air that compiled to native iOS apps... they basically bundle the whole flash player into the game. It was and still is a working way to make an iOS game, it's just that Adobe no longer supports the plugin version... and you can't really trust them to support anything else going forward, so most devs moved to other languages and stacks like Unity.
I think I recall Flash did try to offer some type of iPhone app development features towards the end of it's useful life but Jobs effectively sentenced Flash to death so most everyone had jumped ship by this point.