Source:
Human Rights Watch (U2 likes these guys, and I used to work for them)
Amnesty International has come to the same conclusion. Also look at what Freedom House has to say. There's only about million reports of stuff like this.
Freedom of expression, and any kind of meaningful dissent, is all but dead in Egypt (unless you're a tourist, in a tourist area). Yes, your hypothetical Egyptian atheist would certainly be arrested for speaking out against oppression of women and Christians.
Yeah, yeah. I know. These groups don't know anything about Egypt either.