I heard about an article attacking "new" atheists by reading Ophelia and PZ thrashing the thing quite soundly. Be Scofield makes many of the common mistakes in his critique -- debating strawmen, the Courtier's Reply -- and the atheist defenders make quick work of identifying those errors. Both of them, with Greta piling on, cut out the heart of the article by addressing the central issue of atheism: is religion true? If not then atheism is justified on that basis alone, end of story.
To these excellent responses I'd only like to point out that Scofield's clumsy hatchet job is thoroughly postmodern, and can only be fully understood in that context. Postmodernism argues that truth is a kind of story, so within any community or culture the local truth they all talk about is just as true as different "truths" in other communities. As result postmodernists take the view that Science, with its interest in universal, testable truth, is a kind of western cultural imperialism. That's why he puts "reason" in quotes -- it's just another western product, like blue jeans, to be forced down the throats of less privileged indigenous people who would be perfectly happy without it.
While there may be arguments that some of the prescriptions of modernism may not be appropriate for every social context, that is never an argument to reject the entire progressive project. In a search for objective truth, which must be the very definition of truth if anything is to mean anything, the discovery that a particular idea doesn't always work is just another observation to fold into the search.
The only interesting question that Be actually raises is whether religion on the whole does more harm than good. There could be arguments either way, but they will necessarily be historical. You'd have to weigh the role of religion in Bach's masterpieces against the horrors of the Inquisition, the religious justifications of slave holders against the comfort it gave to slaves, or the religious motivations of those who wanted to exterminate the Jews against the religious motives of those who wanted to protect them. It's by no means obvious that religion would come out on top.
But whatever the result it cannot have any bearing on the question of religion versus atheism. Atheism is not about the past -- it's about how we are now and going forward into the future. Do we value truth, or do we value the not at all certain possibility of comfort over truth? This what's at stake, even if the postmodernists refuse to see it.