In the Justice League Unlimited Season 2 Episode 9, Question Authority, we see that General Eiling tells Captain Atom is reactivated as part of the Air Force.
Next we see we see him, he protects
Claiming that he's operating legally and properly. This leads to Captain Atom
fighting Superman, no holds barred.
What I wasn't clear on was whether or not Captain Atom truly believed he was acting under just orders, or if he was under some sort of mind control from the same entity he was protecting.
I'm not sure if it's said with 100% certainty in the show, but since the events of the DCAU are often based on the comics, swapping out characters here and there, I would be okay with a comic-based interpretation of events.