Similar to dot, I am unfamiliar with a couple of the named "new atheists" (Harris & Dennett to be particular), but yeah, the trend amongst outspoken atheists in recent years has been the wholesale embracing of science as a tonic to the ills of religion. While I am not the sort of anarchist who embraces any sort of spirituality (as many other greenish types are), to embrace science so uncritically simply creates another form of domination - that of "objective truth." Anarchists would do well to avoid that spook as well. So far as I know, this isn't merely a new problem, but has been the case with many atheists (and many anarchists) for quite some time.
On the other hand, I think that focusing merely on the economic, or privileging that over the ways in which social interactions reinforce and recreate domination in our lives is also a dead end. While I reject the political (as politics are understood by mainstream society, as opposed to, say, anti-politics), I also think it is crucial to maintain open dialogue about why politics are a dead end. Similarly, religion (especially Christianity, but the whole Abrahamic tradition more broadly) is not something I have time for, but it still needs to be attacked for it's role in enforcing complacency and domination.
Ultimately, my issue with atheists (as someone who is one), is that there is a tendency to only attack god, while ignoring the state, capital, and other forms of domination. It is exactly the same problem I have when anarchists don't want to talk about patriachy or racism because they distract from the "paramount question." We have to attack all of it.