OK, so the air force asked Cap't atom to stop the JLA from freeing the question (who's nuts). WHY did he do it. reading his origin (I didn't know him from a hole in the wall) Why would he side against the JLA? The air force ruined his life, the JLA gave him a chance to be a hero.
And "It's convientent to the plot and it leads to stupid and pointless fight" doesn't count, he could be the one trying to free Question and supes could be stopping him, that make more sense.