Civil liberties, including the right to privacy, are critically necessary in any free society (the ability to express myself through this site is an obvious example). However, civil liberties do not in and of themselves, supersede national security. By using the term "civil liberties" in this post, I am writing primarily about the right to privacy guaranteed under the Fourth Amendment.
National security trumps the right to privacy when the party imposing security measures (e.g. the U.S. Government) is functioning in the interest of the people it is imposing such measures upon, to protect them from those who would do them harm (e.g. Terrorists). That is precisely the circumstance we are faced with today. I love freedom as much as anyone, but some of the current clamor on domestic surveillance is over the top.