Note: I am not a scientist of any variety, more of a hack wanna be philosopher-writer. I only play one on TV.

I love the semi-scientific bits of Heroes since they let us geeks go and use big words to speculate about things- a longtime pastime o'mine. So, there's of course the immense problem of countering the pressure that one gets on the body when moving at hundreds of miles per hour from a dead stop through rippling air currents.
Let's try methods of explaining the power without having to have Nathan's body be conditioned for flight, which I think would show up on all those physicals the army gave him when he went off to Bosnia.
Now, let's look at aerokinesis, or wind manipulation, the manipulation of air currents. Even if one was to take all the air out of a room- which is quite easy, the room you are sitting in could fit in a scuba tank or a few, depending on how large it is, which an aerokinetic could effectively do by manipulating the air currents in their immediate area, there's still a big problem.
Newton dropped an apple. Oh, how it fell.
Gravity.
This is where manipulation of gravitons comes in.
Gravitons are part of the wonderful quantum field theory(and some variations of string theory, the theory to maybe kinda sorta rule them all maybe...), a
hypothetical elementary particle. Yeah, hypothetical. So we are already reaching for straws. But anyway, gravitons, if they exist and quantum field theory proves to work on gravity as well as it did with the strong and weak force, mediate the force of gravity. In quantum field we diverge from gen. relativity in that gravity and the interactions of it are mediated by a particle(the graviton) and not space time being curved.
I could talk about how they work in String, but even better reading is the theories of Brane cosmology.
All wonderfully interesting stuff for would be physicists, and applicable to Heroes.
To be able to control a single graviton would take quite the effort, theoretically.
First of all, gravitons are like the more familiar photon- 0 mass, meaning they travel in vacuum at light speed. Not exactly somewhere you can just touch and manipulate. Second of all, you can't exactly...see them, thus why they are hypothetical! And detecting them is a lot harder than photons, because photons are sociable, while gravitons sit in the corner and write emo poetry- a low cross section or likelihood of interactions with matter and other particles, and interactions are needed to detect. Third of all, they control gravity, one of the most influential forces in the universe, and a few stray gravitons out of the huge number it would take to fly could do a lot of damage.
Thus meaning if Nathan's power, like many, emerged at an unexpected time and required practice to get to the level we see when chased by Haitian and Bennet...said practice might involve breaking a
lotof stuff. Imagine Sylar's little fun with snow globes, and substitute snow globes for the fundamental forces of the universe.
Despite these qualms, I'll say graviton manipulation is something that should be looked into, by someone more qualified than me definitely.
The thing graviton manipulation, or astrokinesis(control of gravity) has over aerokinesis(control of winds) is that it could negate the potentially problematic- "Why don't his lungs collapse and how can he breathe and etc.?" A "bubble" of manipulated gravity around him, using the gravity outside of that to push himself along would keep Nathan shielded from pressure.
Now, TK. Very much like astro and aerokinesis in core ways- mind manipulating base forces. TK on oneself to fly is a great idea- unless you value your limbs and like living. It still has the pressure problem. Now, TK "fielded" or "bubbled" around the flyer is more promising, a way to negate pressure if used correctly.
As with all powers we have to ask where all this energy to move things all about and make various ruckuses is coming from, and I can put out the usual- tapping into dark matter, photosynthesis, etc, but who knows?
Well, that was a fun excuse to research physics. As if I need one. *Puts cat in hypothetical and walks away*