I have some sympathy for the position that religion deserves some respect, but this does not mean that we should simply bow and accept it.
The problem is that the naturalistic world view is not what most people are exposed to first, and those who are not already on the naturalist side experience the arguments of people like Dawkins as strange and rather alien. Science, like religion, requires an initial leap of faith. The scientific method does not demonstrate its value as a means of making sense of the world until some time after it has been accepted. It takes some experience applying the method to see that it works and how it works. Religion also 'works', by disabling rational argument in certain matters so that the nonsensical parts of dogma don't bother people. The leaves us with a horrible symmetry, where the naturalistic and supernaturalistic world views have little to distinguish them at first approach. Right now, religion is in the better position because few children have a good grasp of science, but religion is easy. Much of what passes for religion is really just fairy tales for adults. The passage from childlike fancy into adult superstition is seamless.
But superstition has about as much to do with faith as masturbation has to do with true love, and literalist interpretations of scripture are mere superstition. Faith is not simple adherance to rote beliefs. There is an essential element of optimism concerning ourselves and others, regardless of its theological content (which may be metaphorical, or entirely redundant.) It both expects and encourages the best in human nature, and makes us more willing to dare and risk failure. "Faith, hope, and charity" are simply different aspects of the same basic attitude. This is the signal in the relgious message. All the rest is just noise.
'Respecting' religion doesn't mean agreeing with it or simply agreeing to disagree. The arguments over the last 200 years that advanced rationalism and secularism were as often fought in religious terms as in secular terms. The success of western civilization stands on two pillars; both Socrates and Jesus chose to die rather than run, fight, or deny what they believed to be true. This simple act I believe to be more important than the specific beliefs they chose to die for--it illustrates an allegiance to the truth, and in the power of truth to win on its own terms. If religious fundamentalists want to play hardball, play hardball back, but do it by proving that they are betraying Christianity. If they don't understand your language, learn theirs. After all, they are trying to prove that science isn't science.
Argument by authority is a fallacy, but an argument that appeals to cultural authority can still be used to destroy a position if your opponent claims to base his argument upon that authority. Fundamentalism is a fortress when attacked from without, but a house of cards when attacked from within. There is nothing more entertaining than watching a secular humanist or moderate Christian well versed in scripture demolish fundamentalist sophistry. You can destroy the symmetry between science and religion if you invalidate bad religion on its own terms. Then all roads lead to science. The goal is not atheism, but an allegiance to the truth and a willingness to follow wherever it leads you. The rest will take care of itself. Ultimately, I think, you can neither prove nor disprove the existence of God, simply because God retreats whenever approached by a refutation, and advances into all empty spaces.
Islam may have a problem here; it is sometimes argued within the Muslim faith that the later positions of Mohammed (when he wanted to kill everyone who disagreed with him) superseded the teachings of his early years (when he preached peace and tolerance.) With this position the religion has been corrupted by a cult of personality. However, what Muslim extremists seem to desire most is a return to the greatness of medieval Islam, and this was the period in which Islam embraced science and reason while the Christians were foundering in ignorance and superstition. If this is their goal, then the fundamentalists are taking Islam in exactly the wrong direction, and they too are betraying their faith.
