[Retracted] You're citing a blogpost from August 2012 for the claim that these bad things "still occur today"? I'm no fan of the atheist movement, and I agree that its proponents can be occasionally lacking in basic kindness and social graces (as do many others, who refuse to self-identify as 'atheists' for this very reason). But still, you're not providing much evidence for your claim here. [/Retracted]
Edited to add: Apparently you only meant to refer to the time 'Atheism+' was actually getting off the ground - the "elevatorgate" controversy and whatnot. If so, I misinterpreted your comment, for which I apologize - but that would make your point rather trivial, since ThrustVectoring was clearly objecting to "Atheism+"'s continued [assumed to be detrimental] influence on the atheist movement.
That was an article justifying the creation of atheism+. This was a discussion of why there was a problem in the atheist movement that lead to its creation.
A long blog post explains why the author, a feminist, is not comfortable with the rationalist community despite thinking it is "super cool and interesting". It's directed specifically at Yvain, but it's probably general enough to be of some interest here.
http://apophemi.wordpress.com/2014/01/04/why-im-not-on-the-rationalist-masterlist/
I'm not sure if I can summarize this fairly but the main thrust seems to be that we are overly willing to entertain offensive/taboo/hurtful ideas and this drives off many types of people. Here's a quote:
The author perceives a link between LW type open discourse and danger to minority groups. I'm not sure whether that's true or not. Take race. Many LWers are willing to entertain ideas about the existence and possible importance of average group differences in psychological traits. So, maybe LWers are racists. But they're racists who continually obsess over optimizing their philanthropic contributions to African charities. So, maybe not racists in a dangerous way?
An overly rosy view, perhaps, and I don't want to deny the reality of the blogger's experience. Clearly, the person is intelligent and attracted to some aspects of LW discourse while turned off by other aspects.