That is because the conflict with al Qaeda is not governed by the Geneva Conventions, which applies only to international conflicts between states that have signed them.
Applying different standards to al Qaeda does not abandon Geneva, but only recognizes that the U.S. faces a stateless enemy never contemplated by the Conventions.
Nonetheless, Article 5 makes clear that if an Iraqi civilian who is not a member of the armed forces, has engaged in attacks on Coalition forces, the Geneva Convention permits the use of more coercive interrogation approaches to prevent future attacks.