Any kind of Atheist Movement would by necessity be primarily composed of people who’ve chosen to prioritize atheism and secularism as a particularly important part of their lives and activism. At first how I assumed this went was people generally thinking “secularism is one of many important issues presently going on, and one that I happen to feel especially passionate about, so that’s where I’m going to be put a significant chunk of my energy and attention”. Cool. And I’m sure lots of atheists do have that as their approach. I’m fine with that, and think it’s important, because we do need a contingent of activists putting significant energy into maintaining political secularism and helping prevent the emergence of theocracy. But lately it seems to me that a much more significant percentage than I’d assumed are people thinking “atheism is the most important issue, so that’s the one I’m going to focus on”.Atheists should be acting like atheism is simply the issue they personally prioritize. Instead, according to Natalie, they are acting as if atheism is the objectively most important issue, or flat out the only issue. Let's call this problematic attitude "movement supremacy", because it's basically holding your own movement's goals as the supreme ones worth fighting for.
Or, worse, when considered in light of the demographics that comprise the movement, “atheism is the only real civil rights issue, because I’m not personally affected by, and haven’t personally seen, any others, so they must either not exist or not really matter. DAWKINS RULES!”
It's very difficult to tell if movement supremacy in the atheist movement, since all we have are our personal impressions of our tiny slices of experience. But certainly it's an attitude that Natalie perceived, and it's one that I have perceived as well, mostly in non-student orgs. Whether this reflects reality or illusion is another question.
Movement supremacy is not confined to the atheist movement, and it is instructive to consider other examples. The first one that comes to mind is radical feminism. And I'm not referring to feminists who are radical, I'm referring to a specific feminist movement which calls itself "radical feminism". Radical feminists have acquired a reputation for subsuming all social justice issues into feminism. Everything comes down to gender-based oppression. And if someone claims that there is a problem that does not fit into this picture, that problem must not really exist.
This is not just an impression based on interpretations of rad-fem rhetoric, it's something you can see in action: Rad-fems are very transphobic because trans people don't fit into their ideas about gender-based oppression. A lot of binary trans people like being able to identify as their true gender, which conflicts with the idea that gender is nothing but a tool of oppression. (Rad-fems have a poor reputation for dealing with asexuality as well.)
You can see why movement supremacy can be more than just an annoyance. Movement supremacists can actively harm other causes.
Feminism is prone to movement supremacy because gender is something that pervades nearly all aspects of society, and thus it is plausible that it is The Most Important Cause. Atheism, liberalism, libertarianism, and conservatism are also prone to movement supremacy because religion and politics are also very pervasive aspects of society. It is harder to believe that heteronormativity or cissexism are the sources of all oppression, so movement supremacy is probably less common among LGBT activists. On the other hand, a few vocal LGBT people complain that cis hetero asexuals don't fit into what they see as the real causes of oppression of sexual minorities. So that's another sort of movement supremacy.
So, back to atheism. The atheist movement is known for having many problems. Women are underrepresented, and there seems to be an MRA-like faction. Atheists of color are underrepresented as well, and it doesn't really get talked about enough. How much of this is due to movement supremacy, rather than other sorts of awfulness? We may never know (and anyways, the question isn't well-defined).
Having participated in at least four different movements, the alternative to movement supremacy is rather obvious to me. My movement's goals are simply those which I prioritize. Maybe because they have personal importance to me. Or maybe because I have the experience or skills to be especially good at it. It is not because my movement is the most important movement in existence, and not because everyone is morally obligated to join my movement. If you don't believe in gods but aren't interested in atheist activism, that's your prerogative. If you think your lack of personal experience with LGBT issues would make you a poor LGBT activist, you may be right. Not everyone needs to be me.