Al Jazeera employees are being treated like enemy agents because that's what they are.
Too many people have spent the last few years pretending to take Al Jazeera seriously as a media outlet. It's not. Its employees are no more journalists than those of RT or Xinhua or the Soviet era Pravda.
Al Jazeera is a mouthpiece for Qatar, a tyrannical state that is notorious for sponsoring terrorists and had links to the attacks of September 11. Like the Saudis, Qatar is officially an ally. Unofficially it's a state sponsor of terror.
In Egypt, Qatar helped the Muslim Brotherhood take over and cut all sorts of dirty deals with Morsi meant to turn Egypt into a puppet of the Al-Thanis. Al Jazeera was a key player in both the overthrow of the Egyptian government and in protecting the Morsi regime.
Yusuf Al-Qaradawi the Brotherhood's homicidal preacher, appears on Al Jazeera from his hole in Qatar, delivering increasingly deranged rants.
So yes, to no one's surprise, the new Egyptian government has thrown the book at Al Jazeera. Their employees are not journalists and anyone calling them that is being willfully dishonest.
Al Jazeera is not a media outlet. It's a projection of state power by Qatar. If you participate in a political takeover of one country by another, you can expect to suffer the consequences if you're stupid enough to stick around when the Egyptians take back their country.
There's a vast gulf of difference between a CNN reporter and an Al Jazeera reporter. CNN doesn't work for the US government.
Al Jazeera employees are agents of a hostile regime. They're being treated like enemy agents because that's what they are.
The new Egyptian government is not remotely tolerant of dissent, but neither was the Morsi regime that Al Jazeera fought to protect.
There is no reason whatsoever to have sympathy for advocates of one totalitarian regime being persecuted by another.