I agree. I have only met scientific fundamentalists in the form of the skeptical community. Although I enjoy their ideas of promoting freedom of thought, their ideas of people having no real purpose really gets to me.
I've met a plethora of religious fundamentalists, as you've probably read in some of my other posts. They really scare me, showing me the darker side of spirituality. I think that both are almost like looking at different aspects of the Borg from Star Trek. The religious fundamentalists run about like members of a hive, all destroying and attacking things that have even the slightest deviation from their theology. The scientific fundamentalists have this mentality that all is mechanical, and there is no real interesting aspect to human existence.
However, like you, I think I'd side with scientists on the question of existence. I think that theology is very wrapped up in human nature.
I think that the rhetoric is definitely hurting their cause. By their, I am referring to everyone that's using it. The religious are alienating more and more people each year through the use or rhetoric. I mean yes, there are all those passionate speeches about the forgiving nature of God and all. But once you're inside, it becomes like a cult, where people like James Dobson and Jack Chick feed on the simple minded - Usually from the pocket area of these people.
According to Richard Brodie, in his book Virus of the Mind, many people are coming out of our schools with a lack of purpose. The rhetoric of scientists is also starting to take its tole.
I think too many people are starting to have knee-jerk reactions to each other. This is likely because in modern history, people have expected that science would provide a quick fix to the problems of the world. Take the various advancements and breakthroughs in medicine. Scientists had not studied bacteria enough to realize that they too could adapt to conditions, and so antibiotics were prescribed as the magic bullet. And so they were for a time. But now we have all sorts of "super bugs" going around. The knee jerk reactions to religious people are no better than the knee jerk reactions of religious people to the secular world. In fact, if we want world peace, or any kind of stability among the human race, the way we're going is not going to cut it. I don't mean to sound too phanatical, but even if science is successful in "eradicating" religion, what will millions of people on the planet replace it with? Won't there be all sorts of people who will rationalize immoral things with "well, we're just a bunch of molecules, so it doesn't make much of a difference what I do"?
Finally, you are definitely right about the complacent certainty. If I am not mistaken, it is complacent certainty throughout history that caused all sorts of heinous wars and genocides. I like what my biology teacher in grade 11 told me:
"Never let anyone tell you 'this is the way it is!'"
He was discussing evolution, I believe, and the interpretations of the theory that are making so many people upset. I think I will leave my ramblings at that for now...