It seems to me he's saying that he hates atheists who don't see atheism as a part of a broader network of commitments or values

And he has a very specific set of values in mind. Something like feminism or social justice warriorism, or whatever it is they call "Atheism Plus". (RationalWiki calls it: "a wedding of the New Atheist's in-your-face attitude about religion with social justice concerns"; and RationalWiki is very positive about this movement, because it's very close to their own beliefs.) And there is some internet drama about it, which I don't follow closely, but it seemed to me that all influential atheists who disagree with Atheism Plus soon get anonymously accused of sexual harassment, and then Atheism Plus fans demand their removal from atheist conventions. Or something like this. And PZ Myers is an important figure there.

Essentially... there is a political faction within the atheist community, and the idea is that the atheists who don't subscribe to this specific political opinion, are not the true atheists. To me it seems that this is not really about atheism, but about a political movement infiltrating another movement which was originally apolitical.

So, if these people dislike (and allegedly fight dirty against) the atheists who don't join their political faction, I would like to see them starting their conflicts with the outsiders under their own flag, not including the people who disagree with them. So that the natural and predictable reaction would be "Atheists Plus are assholes", not "(dictionary) atheists are assholes". If someone starts their own fights, I don't want them hiding behind my back, especially when the next day they are likely to stab me in the back.