And now, of course, the debate has transformed from "why should non-citizens have any rights" to "why should citizens have any rights". I have little doubt that Jonah and company would defend the civil rights of, say, a militia member who was equally hostile to the government (and the secularity) of the United States. In fact, they have: the furor over the militia movement after Tim McVeigh blew up another building prompted loud and repeated calls from the right that the rights of militia members and the like should be respected, whether we like them or not. The same is doubtless true of racists (although the two overlap quite nicely).
And let's not forget Waco, although that was mostly anti-Clinton opportunism.
But, of course, it's different now. Why? Well, that's actually an excellent question. As I mentioned in an earlier update, every criminal is on some fundamental level at war with the state- hence the reason the state has the legitimate right to punish or (in certain parts of the United States) even kill him. There's no difference between an "Al Qaeda operative" and a random street thug... they're both enemies of the state. That doesn't mean that it can lock up people randomly, however: it needs to follow the proper procedure and respect the rights of citizens. Those rights have nothing to do with the severity of crime being charged, who that citizen is, or what they've done. They come with the territory, part of the deal the government makes with the citizenry in exchange for the ability to prosecute and punish crime.
The problem, of course, is that it's incovenient (as civil rights mean nothing if they're only observed when the government wants to observe them), and it's obvious by now that this administration is utterly unwilling to accept even the slightest inconvenience if it gets in the way of what it wants. Frankly, I'm amazed that the Harvard "Jihad" guy hasn't been locked up yet, and considering that this guy is hispanic (and that several of the American Muslims mentioned in instapundit's article I mentioned earlier are African-American), it's no longer just a problem for people who look visibly Arabic. I shudder to think at what the tattered remains of our civil rights will look like six months from now.