I've never taken a side on this issue, but when pressed, none of the anti-conspiracy crowd has ever addressed Project Northwoods and how it could compare to recent events. The best someone has ever come up with is, "This administration is not smart enough to pull off an event this large and complex." Again, this doesn't address the comparison between Project Northwoods and 9/11, but rather, points to an "intelligence" factor with this administration combined with the notion that "hundreds or thousands" of people would have to know about it.
If previous administrations(democrats) could conjure up such black operations under the guise of leading the USA into war with another country, what would stop another administration(republicans) from doing the same thing? Granted, this administration may or may not have deliberately sponsored these "terrorist" acts themselves, but they would be just as liable if they allowed them to take place. The famous line of questioning to Condi Rice regarding the Presidential Daily Briefing over Al Qaida planning attacks in the USA demonstrates they could have let it happen willingly. Why didn't they immediately put into place the strict measures that we have to endure today when we fly??