Okay, so I'm gonna go ahead and be that guy: where was he during the Metropolis battle, then? He couldn't hop in a Bat-Plane and help out? And when Clark showed up at the military base, are we really supposed to believe no one mentioned that other cape-and-costume-wearing guy, or did those mentions just oh-so-conveniently happen off-screen?
That's been an issue in super-hero comics since they started sharing universes. Where were the Fantastic Four when the Avengers were saving the universe? What were the rest of the Legionnaires doing that was so important that there were only five available to take on the Sun-Eater? Suspend your disbelief. The bottom line is that whatever Batman may have been doing behind the scenes, it wasn't relevant to the story at hand. And we don't know that he could have done anything to make a difference. A god-like alien and the U.S. military were on the case. Batman was out of the loop.
And when the military had Superman in custody, they were probably more focused on super-powered aliens on Earth and a possible invasion than on comparing Superman's sartorial choices to that vigilante in Gotham City. Perspective.