Distilled the films punch points ran something like this.
Part One: Man creates false God.
Part Two: Men freed by the revelation of God's contrived nature, use him as a weapon to dominate society. The latest permutation is the Bush White house, who's tactics are cast as unethical.
Part Three: It is implied that the world is Governed by a small group of tyrannical intellectuals who dominate the banking industry and thus the worlds economies.
Part one seems believable. The bible is full of problematic contradictions under the 'Christian' frame of interpretation and maybe a shift in perspective is required to realize the truth of the text.
Part two seems to get a little contrived. Certainly the author/director raises some interesting points surrounding the 9/11 controversy. It seems clear to me that something other than what we were told occurred on that day, but that does not allow us to jump to the conclusion that a small handful of individuals conspired to kill thousands of their own citizens. The shear number of individuals who had to be "in" on the plan is staggering, and seems beyond reason...it would simply to hard to conceal as a secret plan.
A primary correlates is drawn between 9/11 and Pearl Harbor, both the author implies were attacks perpetrated or condoned by the respective administrations. The film delivered an unfair slant on how the events of the day unfolded, stating with absolution that the lack of action was intentional. This is not considered the majority opinion by historians, but it is respected as a potential course of events. At any rate, only rouge scholars would associate the President's inaction with a money making scheme for the Fed. Most often the aforementioned perspective attempts to highlight how Roosevelt snapped Americans from their shortsighted, isolationist perspective (dominant at the time).
As far as part three goes, I think thats absolutely ridiculous. I work for a fund raising firm that specializes in developing fund raising campaigns for philanthropies. Every single day my boss goes out and meets with the heads of major corporations like JP Morgan Chase, CitiGroup, GE, just about anyone you can think of. Additionally one of our biggest clients is the Archdioceses of New York, one of the most powerful Catholic blocks in the entire world. While each of these groups has access to massive amounts of money and influence, the notion that these small groups alone rule the world is absurd. There are thousands of obscenely wealthy individuals that are not cut from this cloth, in-fact, many of the worlds wealthiest people made their money from developing cleaning solutions or distributing food. Whats more important to recognize is that most of the worlds money is 'new money', meaning money that was generated and collected within the last one or two generations. As mystical and compelling as it sounds, there is no secret society of old money turning the world into puppets. Most of the power that used to be associated with the enumerated family names (Morgan, Rockefeller, Vanderbilt) has eroded with time.
Additionally the level of coordination required to carry out this masquerade would require a level of coordination that is beyond belief. It would require that every free thinker be stifled or assassinated. It would mean that the internet was policed, edited, and contrived without anyone noticing or sounding an alarm. It would require that every journalist do exactly as their told. And most importantly it would require that every product, brand image, or facet of commercial society functions to blow smoke into our eyes and cotton into our ears. This level of communication and hierarchical respect is simply beyond the capacity of humanity. The nature of our being human makes us prone to breakdowns and mistakes, and our innate pursuit of individual freedom would tear against this Orwellian scenario the film postulates.
Its good that the film requests that you think; calling that we each ACT upon our realties rather than REACT to them. That said, take the positions forwarded by the film with a grain of salt. Most often the imagination is a tool that runs beyond reality rather than parallel to it.
Learn, think and act. Stand up to fear-mongering, whatever form it may take.