At least with Batman, he wears powered armor when he goes toe to toe with Superman, so I can somewhat suspend my disbelief. Kind of like how Iron Man's suit can absorb blows.
The Flash just wears spandex. I'm sorry, but that doesn't mean he should visibly be seen hurt. If he does have the power to change the properties of his molecules, then have Superman's punches hit air since I assume he can make himself gaseous.
The Flash can do all things through Speedforce which strengthens him. Amen.