As per the storyline of Man of Steel, it is said that Superman is able to fly because of earth's low gravity. But how is he able to control the speed at which he flies? How can he hover or accelerate at any given time?
"I think the best explanation for all of Superman's powers is explained by The Unified Theory of Superman's Powers. It basically says that all of powers Superman has are possible if his power is the ability to manipulate, from atomic to kilometer length scales, the inertia of his own and any matter with which he is in contact.
But as far as applying real world physics there is also a great article that describes it on i09 called The physics of Superman."
Here is the excerpt:
Negative mass and positive mass are supposed to fall towards each other, so he feels gravity the same way everyone else does. However, he also feels air molecules all over his body. If he turned them to negative mass, they would push his body upwards. By contrast, if he turned the outer skin of his body to negative mass (or his aura), the air pressing back against it would cause it to push him forward. So Superman uses air pressure and negative mass to fly around planets with atmosphere.
"Kryptonians are able to manipulate graviton particles, in an unknown and apparently unconscious manner, to defy the forces of gravity. Under one Earth gravity, they are capable of speeds of multi-Mach speeds in Earth's atmosphere. Their control of their flight is very precise and they can perform aerobatic feats such as hovering, flying backwards and even lifting great weights while flying." This is how He does things like this. http://www.fxguide.com/wp-content/uploads/2013/06/MOS-TRL2-2502r.jpg But in Man of Steel, Kal generates his own gravitational field.
Well, in "Man of Steel" you see a disturbance on the ground around Superman just before he takes off each time. So apparently Kryptonians are able to create some sort of anti-gravity field, or perhaps it is a form of localized telekinesis. That would also explain why Zod's henchmen were not able to fly. It would seem that this ability requires a certain clarity of thought or a precise emotional state.