There have been a lot of TV documentaries arguing both sides of the issue, and both can be edited or worded in such a way to 'prove' their case for or against, depending on the agenda of the maker.
Personally, I think it was highly likely to be Al Q'aeda that carried out the atrocities. But the US government didn't help their case by the way it was handled with regard to freedom of information and acting in a very suspicious manner (particularly the Pentagon) that would give free reign to conspiracy theorists who, lets face it, only need the smallest discrepancy to base a whole theory around.
The alternative, which involves the Illuminati, new world order, global mind control... *sigh* I dunno, it seems just a tad convoluted. And if it were a giant conspiracy, there's no way in Hades that it wouldn't have been far more out in the open, especially with how many people would have to be involved in it and subsequently had to keep their traps shut. A whiff of notoriety, and money, and there'd surely have been a lot more canaries singing.
I think it's easier for people to blame something they can see, something they can actually hold accountable like the government itself... rather than a misguided ideal that darts from shadow to shadow.
Better the devil you know...