So what you are saying is that those organizations were operating illegally in Egypt but that because they were Americans they should have been allowed to flaunt the law

"some of the groups that were singled out had operated in Egypt for years and said they were trying to navigate the process of official registration".   Just imagine if an Arab group were to be allowed to operate in the US without official registration.  Not only they would have been close down, all staffers would have been shipped to Guantanamo and Obama would have ordered that all members of their families should be spied on and even droned.