You miss the point. The point of a trial is maybe he wasn't a terrorist after all. Someone who is in fact guilty of certain crimes does in fact lose some of their protections, they can be detained.

Innocent people should be protected from arbitrary detention, therefore everyone should get a fair trial to determine if it can be proved they are guilty, while they have the ability to defend themselves. An innocent person who is wrongly accused of bombing a kindergarten is just as innocent as a person who is wrongly accused of stealing a candy bar.