Again... almost but not quite burningly stupid. New Atheism as an Embarrassment to Atheists repeats the usual canards against the New Atheists. Rather than quote or paraphrase all the stupidity in the article, let me just lay down some obvious truths.
What is New Atheism?
The New Atheists are atheists who directly confront religion as a negative social institution. That's pretty much it. There are critieria — to be a New Atheist you have to be an atheist, and you have to directly confront religion — but there's no dogma.
The New Atheists usually define the sort of "religion" to which we object as institutionalized supernaturalism. Supernaturalism is holding definite propositional (true/false) beliefs about reality that cannot be empirically proven; when an institution uses its power to pressure its members to affirm the supernatural beliefs, then you have a religion in the sense that we criticize religion.
Not being completely stupid, New Atheists understand that, like most other words in natural languages, people use the word "religion" (and other associated words, such as "god") to label a of things to which we do not object (or that we object to for different reasons). It is one of the laziest straw-man/equivocation/uncharitable fallacies to generalize an argument directed towards one use of a word to the word's alternative uses.
New Atheists are not out to convert anyone. We do want to convince people that religion is indeed negative, but we measure our success or failure by the quality of our arguments, not by a count of warm "converted" bodies. Arguments being what they are, and people being who they are, we cannot convince everyone. We are happy to look at counterarguments, but it's tedious and unproductive to simply note that some people, even some atheists, are unconvinced.
The degree to which religion is negative is a matter of controversy within New Atheism. It's actually very rare to see any New Atheist assert that religion (properly defined) is completely negative, and it's rarer to a New Atheist assert that religion is the only social negative. I can't think of any examples off the top of my head, so I haven't cited any; I observe that literally everyone criticizing New Atheists, in general or specific individuals, for asserting that religion is completely negative or the only negative never offer valid citations. (They usually cite Dawkins, who has explicitly disclaimed both positions.)
Unlike most religions, New Atheism does not have any kind of institutional structure. When you have an institutional structure, when a member of the institution acts (or speaks) in some particular way, and the institution does not effectively condemn that action, then it is reasonable to infer that the institution approves of, or at least tolerates the action. Because there is no New Atheist institutional framework, this analytical method is inappropriate. If you want to make generalizations about New Atheists, you have to do the difficult academic work of searching for pattern in many examples, and looking honestly for counter-examples. Or, you can just criticize individuals, which is easier; if your criticism is valid, it is useful. If it's stupid, it's still valuable, just not in the way you might expect.
Non-problems in New Atheism
There are several reasons why Hitler, Stalin, Pol Pot, etc. are just not a problem for atheism in general and New Atheists in particular, but the most compelling reason is that there's no there there.
First, there is a lot of evidence that Hitler was actually religious, fusing Christianity, pre-Christian Northern European polytheism, and German Romanticism, and inventing some of his own religious bullshit to add to the mix.
Contrary to the assertion in "New Atheism as an Embarrassment," there is no evidence whatsoever that atheism per se has motivated any socially organized violence, even legitimized violence (e.g. law enforcement, self defense, etc.). All cases of politically legitimized secular persecution of clergy and religious worship has been where religions and clergy posed a threat to the legitimacy of the regime.
Establishing and maintaining legitimacy is an enormously complicated topic in political science. There are a lot of interesting arguments about how governments do and do not — and how they should or should not — establish and maintain their legitimacy, but atheism is an issue only when governments establish legitimacy on supernatural grounds.
Problems in New Atheism
There are a few real problems in New Atheism. First, it really is dominated by a lot of privileged old white middle-class capitalist men. To a certain extent, that many prominent New Atheists have considerable social privilege is inescapable: people with privilege have a much easier time challenging social norms precisely because they have privilege. The lack of leadership among New Atheists makes it both easier and harder to be inclusive. Easier, because there's no institutional framework that can exclude women, people of color, queers, communists, etc. Harder, because there's no institutional framework that can fast-track inclusion.
The issue of misogyny is more important. In the last year or so, as atheist women (e.g. Greta Christina, Rebecca Watson, and dozens of others) have pushed for full inclusion in the general atheist community, they have faced an astonishing backlash of the worst kind of slimy, reprehensible harassment by people who call themselves atheists. Lacking an institutional framework, there is no way to "officially" exclude these assholes. They are being fought, however, and socially excluded as best we can. But misogyny is hardly unique to atheism; as slimy and disgusting as the misogynist atheists are, to my knowledge no atheist has thrown acid in a woman's or girl's face, nor assaulted, kidnapped, or murdered any women or girls, nor implemented any form of institutionalized political oppression or persecution of women. Even at their worst, atheists seem to have at least a bit more self-restraint than many theists. Maybe it's just that the misogynist assholes don't have institutional and political legitimacy, but the strong opposition to misogyny, a strength of opposition seen in few institutionalized religion, is precisely what is blocking political legitimacy.
The Fundamental Asymmetry
There's a fundamental asymmetry between theism on the one hand and atheism in general and New Atheism in particular on the other. Religions are, by definition, institutions. Religions claim guidance from a typically perfectly just, perfectly loving, omniscient and omnipotent deity. Religions claim special authority for specific individuals to learn, understand, and communicate the deity's moral demands. In contrast, New Atheism is not institutionalized. We claim guidance only from finite, imperfect human reason, using minds which we know have all sorts of biases inherited from our evolutionary past. New Atheists claim no special authority: our arguments are out there for all to see; there's no hidden knowledge that can specially legitimize any individual's argument. Almost all the arguments against New Atheism that are not just flat out lies and bullshit usually assume that we are institutionalized, that we do claim the sort of divine certainty that many many religious believers and leaders do indeed claim, and that some individuals, such as Richard Dawkins, have some fundamental epistemic and moral privilege. These kinds of criticism are nothing but projections of religions own fundamental flaws on a group of people who categorically reject those flaws. When theists project their own hangups on us, they do nothing but embarrass themselves.