From the time that someone figured out that the sun was not a chariot driven across the sky by Helios, science has been in the business of replacing supernatural explanations with natural ones. Religion has occasionally slowed the process, but it has never stopped it. More importantly, it has never made the process work in the other direction. Nevertheless, the Intelligent Design folks think that they can get science to pull off this unprecedented feat. In a way, their confidence in science's explanatory power is far greater than that of the most committed naturalist. While I admire their chutzpah, I doubt that they will be successful.
Damon Runyan wisely observed "The race is not always to the swift, nor the battle to the strong, but that's the way to bet." I don't think that the antipathy towards Intelligent Design has anything to do with suppressing free speech. I think the scientific community reasonably views ID as a quixotic pursuit whose probability of success lies somewhere south of perpetual motion and the transformation of lead into gold. I would not expect research universities or peer reviewed journals to support tilting at windmills.
What I have found most fascinating is the credulity of evangelical Christians when it comes to the contents of Expelled.* I will admit that I am favorably inclined towards liberal filmmakers like Michael Moore, but I realize that he is prone to hyperbole and I certainly would never cite one of his films as proof of any fact in a discussion with a conservative. I would realize that I would need to verify his claims with some reasonably independent source because I fully appreciate that people who share my views are fully capable of shoveling manure. On the other hand, before the film even opened I was being challenged by evangelical Christians to watch the trailer for Expelled as if no reasonable person could fail to be convinced by that alone.
*I would like to salute ChrisB over at Homeward Bound for considering the possibility that the movie needs to be taken with a grain of salt.