It is still a mistake for the Obama administration to do so:
The U.S. government has never been shy to criticize Iran over its dismal human-rights record, particularly since Tehran launched a crackdown on opposition voices following last summer's election. But the U.S. stance remains considerably more subdued when Egypt, Washington's biggest Arab ally in the region, exercises similar bad behavior. And the months ahead will test just how subdued it intends to be.
All we do is align ourselves with the despot against the people. Which is fine "foreign policy realism" as long as the despot is winning. But if the people finally rise up, you have a revolutionary Iran type situation at the heart of the Arab world with revolutionaries who have no reason to love America and every reason to hate us.
Long term, we need to push Egypt to reform and show that we are not just supporting a repressive regime.