Ezra Klein in the Washington Post:
These guys took down a plane with box cutters. They used crude weapons to attack a far more sophisticated and effective fighting force. The most fearsome of them was captured at home, in his pajamas. It's not like we're putting Magneto on trial and need to keep him away from metal filings.
It's one thing to be afraid of terrorism. But there's no real reason to be afraid of terrorists, and as Daphne Eviatar argues, there's good reason not to look like you're afraid of terrorists:
The contrast of seeing these ordinary-looking men on trial in an orderly U.S. courtroom — where they’re accorded the right to a lawyer, the right to speak in their own defense and the right to call witnesses — could go a long way toward publicly revealing the absurdity of their cause, as well as the justice that a fair and functioning legal system can provide.
Trying these guys publicly, as well as holding them in normal prisons like common criminals, is good public relations.