I dont think Dawkins is suggesting we literally form an atheist militia, but it is strongly implied that atheism and science need to be rigorously defended under the growing onslaught of attacks from the ignorant religious right. The attacks are particularly insidious because they do not occur in the form of intellectual challenges or debating points (which I think most Scientists and Atheists would welcome), rather, they take the form of propeganda outside of forums to the illiterate and under-educated, children etc. They take the form of backroom deals cooked up in churches and pushed into government policy directly past open public scrutiny.
These religous attacks literally circumvent accountability to intelligence by operating well away from the light of public inquest. The damage from the attacks is spreading ignorance, illiterate and undereducated generations, and thus a general increase in crime, violence, support for unjust wars, and the ablity for corporations to take advantage of a large, undereducated voting bloc to effectively rob taxpayers blind while "praising jeebus" in public.
This is why "militant" atheism should be discussed and defined...we need to proactively do something about the cancer of religion and ignorance.