Don't assume that the cartoon versions are perfectly accurate all the time.
Capt Atom is meant to be amongst the physically strongest heroes on the planet. He is actually meant to be a human being below a layer of alien metal that his body absorbed, not a glob of energy as the cartoon would go on to show.
He is incredibly durable , probably even more durable than Superman against energy (as he would absorb it and get catapulted through time in to the future if the blast is big enough), but he is far less durable than Superman to kinectic energy i.e. punches, which he can't absorb. So in this instance, with all the damage showing up on Atom, that is accurate. He also lacks Supermans super speed reactions, just to make the fight a bit more 1 sided.