It didn't stop John Adams or FDR, either. And there's a whole wonderful history of Constitutional law mapping how in each case the courts walked back those limits.
What appears to happen is this: as a threat is seen as real and significant, the public freaks out, the politicians forget the Constitution and shred the target's rights, the courts turn a blind eye until the hysteria passes and then reassert civil liberties. Basically, those First Amendment protections we all think make the US special and America free? Turns out they're very elastic.
Now this doesn't sound like a very solid protection for our liberties, but it's worked OK up until now. For one thing, if the Court ever went up against the other two branches in a time of perceived national emergency, the public would turn against the court. Fear turns any public into a mass of gibbering idiots, so the only way for the system not to seize up is to let the demagogues have their way for a time. If we ever see another major terrorist attack on US soil American Muslims are going to wish they were 40's Japanese Americans. We already saw a wave of blind madness roll over the country after 9/11 which was shocking but, by standards of real destruction, nothing.
We have been a free people mostly because we have been lucky. Whenever civil liberties have been tested against fear, civil liberties have lost until the fear has ebbed. The only consolation is I can't think of a country that has protected the bulk of its citizens' liberties for a larger proportion of the time. But then again I also can't think of a country that has had it so easy up till now.
