The military itself has no real political affiliations, to the point that it did absolutely nothing to stop the popular uprising. Mubarak had to go back to his old standby of hiring goons to beat up protesters, because the military didn't give a single fuck. Near as I can tell, the military doesn't want to be in charge, it just feels it's necessary for the moment.
"If an injury must be done to a man, it should be so severe that his vengeance need not be feared" - Niccolo Macchiavelli