This is very interesting do you think Hillary Clinton is going at odds with Obama?
Here is another article about Obama vs State Department stances on egypt as an ally.
"I don't think that we would consider them an ally, but we do not consider them an enemy," Obama said, reacting to the ongoing and intense demonstrations outside the U.S. Embassy in Cairo.
The State Department, cutting through the confusion over President Obama's claim that Egypt is not a U.S. ally, contradicted his characterization Thursday. For the record, spokeswoman Victoria Nuland said, Egypt is considered a major non-NATO ally.
http://www.politico.com/politico44/2012/09/state-dept-egypts-still-an-ally-135479.html