He didn't fly through time. He reversed the Earth's rotation, thus reversing time. This is all of the information the film delivers to the audience; Superman flies around the Earth, the Earth stops, the Earth begins rotating in the opposite direction, time is reversed.
Evidently, the reversal of time is a consequence of the manipulation of the Earth's rotation, and not by Superman traveling fast enough to transcend time and move into the past. Heck, after time is reversed, Superman even flies around in the opposite direction in order to readjust the rotation.