I don't think the intent of this documentary was to evangelize so much as to present a point of view, and even more to put out there a sort of flag in the sand. One does not have an interview with the likes of Ted Haggard with the aim of converting him, nor was in done in such a way as to cause people currently following him (or, who were following him at the time - Ted managed to bring himself down quite effectively, after all). If he were interested in bringing down fundamentalist preachers, he'd be taking the same approach as the Amazing Randi - who once took a radio scanner into a revival meeting and captured the preacher's wife prompting him so that he could seem to just know the names and afflictions of the various people.
Dawkins has explicitly admitted that his more confrontational style is at odds with the more conciliatory views adopted by the late Stephen Gould (who advocated NOMA, or Non-Overlapping Magesteria, indicating that science and religion should not be considered competitive because they are talking about entirely different subjects). He would also dispute the theistic interpretation of evolution - that evolution is an acceptable theory, but that it is merely the way God chose to work. He fully acknowledges that such compromise positions are entirely appropriate if your main goal is to make sure that science, rather than Christianity, is taught in public schools. His goal, on the other hand, is to force into the public square the issue of religion itself, which he sees as a (not to use too loaded a term) clear and present danger to values that have defined Western civilization since the enlightenment. The less extreme you think the situation currently is, the more over the top you will find his behavior.
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JBS Haldane's Four Stages of Scientific Theories:
1. This is worthless nonsense.
2. This is an interesting, but perverse, point of view.
3. This is true, but quite unimportant.
4. I always said so.
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