Adding to all other comments, a lot of the suspicious Bush administration's immediate reaction (i.e. PATRIOT act) can be understood as them being always ready for whatever calamity in order to justify either invasion or neoliberal "reforms".

Naomi Klein (liberal) goes into detail in her book (Shock Doctrine) about what she calls "Disaster Capitalism" and how a lot of effort is put into laying down the groundwork, both legally and ideologically, for whenever crises make them possible, besides constantly agitating for chaos which can lead to said crises.

She has a documentary which summarises her book, if you want a peek. You can easily draw parallels between the events she describes and what's happening now in Argentina, Ukraine and Ecuador, among others.

Now, with regards to what motivates this conspiracy theory: it's a patriotic distraction. As US citizen lives are treated by US society as inherently more important, portraying Bush as a traitor is an attractive pitfall to fall into, whitewashing the constant crimes of the US, internally and abroad, as the acts of "a bad president". Even if Bush had personally pushed a button to launch missiles at the WTC, it would not be even remotely close to the social murder caused by his administration, or any other admin before or after.