Obama does take sides. He seeks to assert US influence over whoever wins.
Part of this struggle seems to be about Egypt becoming an independent country with its own agenda.
With AQ, pushing foreign influence aside is the explicit agenda. The Moslem Brotherhood thought it could be done peaceably. AQ says it requires violence.
Unfortunately, it seems the Egyptian army is pushing the Brotherhood into the exact alliance we don't wish to see. Not very smart.
So O sits on his hands. He may not like it but history doesn't always favour passive responses. Sometimes you have to take a side.