"Out of" can be used several different ways. For example " we are out of steak" means we dont have any more steak. "the machine is out of order" means the machine is not working. "Johnny, get out of the box!" means to get out from being inside the box. "Out of" in that case assumes something was inside of some place. It would sound strange to say "Johnny, get out from the box", you would need to say "Johnny, get out from inside the box". Since "out from" means more to "get away from" than inside.