You will say that a group has the right to call themselves whatever they want, and you will be right. I just wish they hadn't chosen that term. It extends this group's screwing up cultural battles that don't need to be fought into yet another realm I care deeply about, and as with the first, it can only make things harder and more complicated.
Who are the "gnu atheists"? Well, first, a word of warning. If you try to define them, they show up and accuse you of choosing a definition for purposes of setting up a straw man. However, most of those in the movement formerly known as "New Atheism" seem to share the following characteristics. They are atheists. They believe the world would be a better place if religion would go away, becoming nothing more than cultural history and cultural tradition. They think that any religion that claims to be anything other than just cultural tradition is incompatible with science and the scientific world view. They believe that if somebody aims to accept science and is intellectually honest and consistent, the success of modern science must necessarily lead that person to accept philosophical materialism. They use the word "reason" as a synonym for "application of scientific reasoning", thereby making anybody who is religious by definition guilty of thinking without reason. (As well as a lot of other people, for instance all faculty at a University who aren't in a science or engineering department, but they tend either not to realize that they're doing it, or to downplay that.)
Beyond that, a subset of them are incredibly strident and combative. They think that any religion at all is a threat to science. They do not hesitate to call non-atheists idiots or childish. They will crap the comment threads of posts like this one with all sorts of (frankly) bigotry hiding under the clothing of assumed "reason", citing the names of logical fallacies the way fundamentalists cite scripture. They will assert that they know the Truth and that therefore it's perfectly justified for them to say frankly insulting things, and then say that others shouldn't be offended by the Truth. They seem to think that non-fundamentalist theists are prevaricators who "pick and choose" from their religion, and thus are somehow misrepresenting their own religious beliefs. I generally think that this is because they'd prefer to argue against fundamentalists, for it's extremely easy to show how fundamentalists are at odds with science. But, it's very disheartening to see somebody who wants people to accept science then criticizing a theist for not being a fundamentalist. It is the behavior of this subset that leads me to the conclusion that "fundamentalist atheist" is the best term for this sort of atheist. Most atheists, thankfully, are not like this, but there is the subset that argues that their philosophy is the only philosophy that can be accepted by reasonable people who accept science— much as fundamentalist Christians argue that their philosophy is the only philosophy that can be accepted by people who are good and "saved".
What is the first cultural battle that these "gnu atheists" make more difficult? Well, obviously, the whole religion/science debate. Given that a substantial fraction of the USA is religious and values their religion, it should be pretty bloody obvious that if self-styled defenders of science are out there saying that science is incompatible with religion, it is only going to put up more barriers against the bulk of the population accepting science. Of course, sometimes obvious things are wrong— quantum mechanics is full of examples. And the new atheists are fond of pointing this out, arguing that there is no evidence that what they're doing is harmful. Of course, there's also no evidence that what they're doing is helpful... but they don't seem to think that a lack of evidence coupled with what is obvious disrespect and very plausibe harm is enough for them to question their behavior. What's more, when you do present evidence, they will often dismiss it as anecdotal, or not clear statistical evidence, or not enough evidence, in a manner that frankly reminds me of this comment on Phil Plait's blog by a creationist who insists that without complete timeline of all mutations in evolution, one shouldn't accept evolution. (Aside: despite having the same first name, I did not write that comment!)
These "gnu atheists" will attack defenders of science such as the Chris Mooney & Sheril Kirshbaum, or Josh Rosenau, for pointing out the obvious harm that their tactics could do to our shared cause. They will argue that the National Center for Science Education shouldn't be saying that science and religion are compatible, because if they're really about "science" they shouldn't be saying anything about religion at all. This last tactic is particularly annoying, because of course they themselves will not hesitate to go out and say that science is incompatible with religion. After all, the way that they've defined things, they're just telling the truth, and anybody who claims to defend science and says that religion might be OK is venturing into off-limits territory. They will reject empirical evidence that religion and science are compatible— specifically, that huge numbers of working scientists are themselves religious— on the basis that it is incompatible with their philosophy, and therefore non-atheist scientists have something wrong with them (they're "compartmentalizing", or "intellectually dishonest", or some such).
So. We've got a cause that a lot of us care deeply about— mainstream acceptance of science, scientific reasoning, and the scientific method. We have those out there— fundamentalists of various religions, most obviously— who want to reject much of science, and who have a distressingly powerful voice in public political discourse. And, we've got a broad population who are religious and care about their religion, but who are capable of accepting science. Then, we have a subset of those arguing for science who also argue that accepting science means having to reject religion... which of course provides direct support for the fundamentalists who argue that scientists are cultural warriors trying to take away everybody's religion. That's not true, but the fact that some scientists are out there saying that makes it much harder for people like the NCSE to argue that the scientific establishment really doesn't want to destroy religion.
In other words, I'm annoyed at the "gnu atheists" in the first place; not just because many are so blinded by their love for their own philosophy that they can't see that it isn't necessarily objective truth, and not just because many are frankly rude and insulting while thinking there must be something wrong with me if I find them rude and insulting. I'm annoyed at them also because they're getting in the way of a cause I care about, mainstream acceptance of good science and scientific reasoning. There are a lot of religious people out there who have no problem with evolution or the Big Bang, and there are a lot more who wouldn't have any problem with it if they really learned about it and learned how Christians like myself are still Christian while accepting all of science. Those people are people we should reach out to. Telling them that religion is idiotic, or intellectually dishonest, and that the real people who accept science must all be atheists, isn't going to help.
What's the second issue? Open source and free software. "Huh?" you may say? To be honest, I don't know the etymology of the recently-arisen term "gnu atheism", but I'd wager that it's taking the term "new atheism" (which caused all sorts of boring pedantic and semantic arguments) and riffing it together with Gnu of the Gnu project. The Gnu project is one of the original projects that pushed the notion of open source and free software, long before the term "open source" was coined. Much of that movement today would not exist without what the Gnu project had done. A lot of the core software you use on your Linux system was written under their auspices. But, more importantly, the Gnu project gave people like me, people who have a strong ethical attachment to the notion of free software, a central place to rally around. And, crucially, they provided the Gnu Public Licence, or GPL, one of the most important and most widely used free-software licenses.
Of course, there are some in the business world who see free software as a threat. So, there have been, and will continue to be, disinformation campaigns that try to link free and open source software to other dubious and/or Unamerican things, such as communism, computer crime/hackers, rampant disrespect for copyrights, etc. It's a complete misrepresentation to say that there is a conflict between "the interests of business" and free software, but that is a narrative that's out there floating about. What's more, those who tend to care about "the interests of business" are likely to be, at least in the USA, on the "right" side of the political spectrum in the common but flawed one-dimensional model of political opinion. Those who are religious and worried, or potentially worried, that the scary scientific mainstream is trying to destroy religion are also more likely to be on the right side of the spectrum.
Put it together. You have this movement out there, the subset of atheists whose stated goal is to destroy religion and who assert that complete and intellectual consistent acceptance of science requires a rejection of religion. That is a movement that people who aren't already atheists are likely to view with suspicion. Now, they've taken a name that seems to link them to something that is completely separate, open source and free software. It bugs me already for aesthetic that these guys have hijacked the term "Gnu". But it can't help but create a link in some folks' minds between this crazy hippy dubious philosophy about sharing software you've written to attacks on religion. In sort, free software may now be perceived as having something to do with yet another cultural assault that, frankly, has nothing whatsoever to do with free software. "GNU public licence? Isn't that related to those scientists who want to destroy all religion?" Sigh.
Life is hard enough for those of us who want the world to accept science, and for those of us who want the world to at least be compatible with free software. It only gets harder when some act in a way that is basically the caricature of what our opponents already claim we are.