In Daggerfall an dragon explain thats dragons use their voice for levitation magic and dragon by self says thats their physiology don't allow them fly well without magic.
Too bad Dragonborn cant learn such shout.
Look at it this way. Dragons 'evolved' in a world where magic exists. They could have been intelligent lizards who learned levitation magic or even jump magic to help them get at prey. The wings are extra appendages - dragons came from a four-legged beast who kept all four legs and evolved two additional 'arms'. (Or perhaps the original forelegs developed into the wings and the forearms are the new arms? Hmmm...) At any rate, stir in extra mutations possible through magic, and dragons could exist today.
It is also quite possible that dragons also developed shield and resistance magic to counteract their weak, lightweight skeletons. You might think of magic as spells that are cast or powers used, but such magic that evolved into the creature is as automatic as breathing. They don't have to think about it - it's 'natural' in the world of magic.
This explains why dragons are so tough while they are alive - their magic sustains them. Once they are dead and that spark of magic dies, the are just as vulnerable as any other lizard.
Hope this helps!
Sus