They did that for decades. The crackdown was huge after Sadat was assassinated. I remember a story a while back (here on FR) of some Islamic terrorist in Egypt custody who apparently committed suicide by repeatedly ramming his head into the wall. They tried to stop him, honest.
Nasser banned the Muslim Brotherhood, and always fought with them.
Although I support the rights of Christians and secularists in Egypt, there is something manipulative about this situation, and it is as if they are being set up as the impotent public face of an unknown power. The Muslim Brotherhood did win that election, and represent a large sector of the population.
We do not really know who is behind this coup in Egypt. It may be forces similar to those who went into Benghazi, with a well armed expert strike force, and sprang a CIA safe house, as well as their escape base. There is something going on, and we do not have even half the story.