This guy, Steven Jones (no relation to Alex), wrote a scientific paper questioning the official story.
He's a professor of Physics at Brigham Young University. No, he doesn't go right out, at least here, and accuse the U.S. Government of staging the attacks, but does criticize the flaws in their investigation.
I dunno, anyone who is interested in this kind of things and has the time and attention span should check this out. It seems to have more credibility than "Loose Change" or Alex Jones, etc.