After checking out his webpage and that essay, I realized that I've actually read one of his books before (Agents of Repression).
In Agents of Repression, he attempts to prove the basic thesis that the FBI is not a crimefighting unit but an agency designed to stifle and repress political dissent, and has been working toward these aims since it's inception. It's a very difficult thesis to prove, but he does an admirable job defending it.
In this case, his arguments are being blown way out of proportion. I'd never read the essay before now, but the media references to this guy as "the professor who compared WTC victims to nazi's" is certainly misleading. He chose to reference 'combat teams' in order to highlight a worldview that we generally aren't exposed to.
Churchill does say some things that are undeniably accurate. For instance...
Nor were they "fanatics" devoted to "Islamic fundamentalism."
One might rightly describe their actions as "desperate." Feelings of desperation, however, are a perfectly reasonable – one is tempted to say "normal" – emotional response among persons confronted by the mass murder of their children, particularly when it appears that nobody else really gives a damn (ask a Jewish survivor about this one, or, even more poignantly, for all the attention paid them, a Gypsy).
That desperate circumstances generate desperate responses is no mysterious or irrational principle, of the sort motivating fanatics. Less is it one peculiar to Islam. Indeed, even the FBI's investigative reports on the combat teams' activities during the months leading up to September 11 make it clear that the members were not fundamentalist Muslims. Rather, it's pretty obvious at this point that they were secular activists – soldiers, really – who, while undoubtedly enjoying cordial relations with the clerics of their countries, were motivated far more by the grisly realities of the U.S. war against them than by a set of religious beliefs.
This is basically true. When we blame the attacks on "Islamic fundamentalism" and laugh about the sheer absurdity of dying in the hopes of 72 virgins we do ourselves a disservice by reducing the conflict to something much more simple than it is. In reality, violent Islamic movements have arisen because of a complex variety of economic, social, and political factors. While we may disagree with Churchill's characterization of "the U.S. war against them," we can certainly say that an Islamic terrorist is more likely to think of himself as a soldier fighting back against the oppression of Western imperialism than he is to think of himself as a religious nutcase bound for martyrdom.
In predicting and explaining the character of these conflicts--
the primary job of a political scientist-- it is important to understand the mentality of the participants. Conflicts often arise partially because of issues of group image and group identity. Participants have a set of expectations and beliefs about themselves and their enemies that may not necessarily accord with reality. The fact that these images are not wholly accurate does not undermine their importance in creating, sustaining, or eliminating violent behavior. As such, studying them is extremely important in order to reduce violence now and prevent it in the future.
This man has clearly gone beyond academic objectivity and begun to present events from the perspective of the middle east. He is, however, providing a semiaccurate account of the actual motivations of one of the actors in this conflict (a generalized account of the motivations of assorted militant Islamists). Furthermore, he is closer to being objective than many pro-American academics are-- it just so happens that he's on the other side. He has no obligation to consent to the actions of his government, and should have none, whether the taxpayers are paying him or not.
It is easy to overreact to him because of his crude and insulting language regarding the United States. He makes the mistake of taking the problems created by the modern international system and attributing them directly and personally to politicians in the United States. The important thing to keep in mind is that many commentators make the same generalizations and use similar language regarding the Middle East, and these commentators do not describe the Middle East any more accurately than Churchill describes the United States. Furthermore, the world view he presents is a world view that a great many people share, and these people are taking actions that have greatly affected our country. To refuse to recognize the fact that this world view exists has reached beyond stupidity and near suicide.