He was born on another planet, Krypton, and sent to earth as an infant, as he matured the powers developed
the reasons have been one of the 2 following
1: Krypton orbited a Red sun, and so being born for a life under a red sun, when he spends time under a yellow sun, the variant radiation of the 2 stars causes hims to be faster, better, stronger, etc, than Humans who were born under and designed(or evolded) to live under this type of sun.
2. Krypton was a far larger planet and had a great gravitational pull so in order for life to function, anything that lives must develop stronger bones, denser muscles, and an all around 'tougher' anatomy so that they could function within the greater constraints. (think of how on the moon astronauts could jump higher, and throw things farther than they can on Earth) so too then does Superman hit harder and move faster on the Earth he used to simply jump, which evolved into flight within the comics
The gravity explaination does not explain x-ray/heat vision, but then again its the comics, and when it was cited, no one thought that fans like us would as such a silly question.
I think the Variable Sun as the source has officially been cited as canon for several decades now.