Well worth a read. The point is that apart from cases like al Qaeda fighting in Afghanistan alongside its (erstwhile) national government constituted by the Taliban, terrorists are criminals governed by criminal law (innocent till proven guilty, need to be charged with a crime and have their day in court, etc.) and are not enemy combatants (e.g., prisoners of war).
A person suspected of crimes in the context of his association with Al Qaeda must be charged with a crime, and put on trial with a reasonable opportunity to establish his innocence of such crimes. Because remember, just because the government SAYS you are a "terrorist," doesn't mean you are. Our centuries-in-the-making legal system requires the government to prove its case -- as well they should.
C.G. makes the observation
They complain that the rule of law gives certain advantages to insurgents and outlaws. They're actually right about that. The rule of law is what prevents any government -- and the hegemonic forces that support it -- from becoming what we would call "totalitarian." It is what forces any government to confront political opposition by means other than force. It is what promotes and leads to "political solutions" and forces otherwise coercive government to deal with grievances, and build broad based support.