Michael Shermer, in a Scientific American article entitled Rational Atheism pleads for Atheists to remain polite and tolerant toward Theists. He is not pleading so much for rational thinking as for unemotional politeness.
Shermer states that, "Since the turn of the millennium, a new militancy has arisen among religious skeptics in response to three threats to science and freedom: (1) attacks against evolution education and stem cell research; (2) breaks in the barrier separating church and state leading to political preferences for some faiths over others; and (3) fundamentalist terrorism here and abroad."
You neglected to mention intolerant propagandism against all things included under moral liberalism, Michael. In this category are included, in alphabetical order, the religious right's anti-abortion, anti-atheism (a new target), anti-individual-rights, anti-gay, anti-liberalism (as an attitude), and anti-science (not merely biological evolution and stem cell research, but attacks on the credibility of science).
Shermer's reasoning: anti-something movements by themselves will fail; positive assertions are necessary; rational is as rational does; the golden rule is symmetrical; and, promote freedom of belief and disbelief.
Unfortunately, Shermer is incorrect that anti-something movements fail. The religious right holds wrote the text on Antiism. The Religious Right has too successfully employed the Internet and the media's love of controversy to promote its own Anti messages.
Most individuals have a moral sense that they acquired from their parents, and sometimes in antagonism to their parents. However, the fence-sitters can be swayed by vehement emotional protestations and inaccurate language (abortionists "murder babies", for example).
The lay public, of whatever religious conviction, has been so exposed to disinformation about science that many individuals simply have no idea what to think. Further, religious individuals tend to believe what they are told to think. This, after all, is what religion is all about.
Scientists have made many positive statements about science. However, these messages have been made in language beyond the layperson's comprehension or published in comparatively inaccessible places.
We ought not to make personal attacks on the person because of his or her beliefs. However, for areas that are not a mere matter of value-based opinion, this does not mean that the content of those beliefs should be held sacrosanct.
The dichotomy is clear – either the supernatural cannot exist and all is natural (physical) or the supernatural exists (whether or not any religion has elaborated a correct interpretation).
Lower-case atheists simply do not believe in God, agnostics say we cannot know, and deists and theists insist on including the supernatural within their worldview.
We A-Deists maintain that supernatural beings or forces neither exist nor could interfere with the physical realm without becoming part of the physical. That is, if the supernatural does exist, it has no more relevance to life on Earth than events at the far edge of the universe.
St. Elsewhere : Skeptician's Opinion on Atheistic Expression : Open letter to Michael Shermer in response to his letter (Brian Sapient, Rational Response Squad)