Also, there's the obvious, cynical "cui bono?" point. The government is one of the few entities that could reasonably be said to have benefitted from the attacks (expanded power, pretense for war, &c.), so if you start with the assumption that the "official story" is wrong the government would be the next most plausible culprit.

The argument used is much more applicable to creationist arguments of the form "evolution has this flaw, ergo god exists".