As far as I can tell, there kind of is a scientific theory on how we can move faster than light, although really we're not moving at all. It's what they're working with to make hyperdrive things and allow us to properly explore the universe; allow us to get from Earth to Alpha Centuri in a week rather than countless millennia.
The idea is there is matter in the universe that, much like water, is displaced by physical things. Using something that pushes this matter away, the engine would basically move the universe around it, thereby displacing us rather than us actually moving. If you're looking to apply that to comics, then you could say that the Speed Force or whatever kryptonian biological function permits Superman to Fly, and that there's not horrendous Sonic Boom when they do, then you could say it is basically manipulating this matter around them when they run/fly.
That, and the Speed Force allows the various Flashes to manipulate their own molecules to vibrate at various speeds, and that kinda gets into a territory that I have no way to explain. In any case, this allows them to phase in and out of physical reality and time travel.
This is what I was thinking of (and yes, I am aware of the thumbnail >_> ):
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