I'm really late to this one, but PZ Myers had some posts criticizing Greg Epstein's humanist chaplaincy. If I read PZ correctly*, he doesn't like using a church-like model for community organization. If you want to read more, I recommend Crommunist's response (which inspired parts of this post).
*It is entirely possible that I misread him.
I think of this as atheists stumbling over their own rhetoric. Atheists openly criticize many aspects of religions, and for plenty of valid reasons too. But atheists, being human, will make mistakes about which aspects of religion cause it to be so bad.
For example: I've heard lots of atheists jokingly say that atheism is great because it frees up your Sundays. If these are the kind of idle jokes you make, you might have a negative reaction to atheist groups that have weekly meetings, particularly if they're on Sundays. But is that really what's wrong with Christianity, the mere fact that there is a tradition of Sunday meetings? Obviously not... But the rhetoric is there, and we're stumbling over it. And it sure doesn't help that outsiders will stupidly grab onto any similarity between atheists and religious people, as if that were a valid criticism of anything.
This may be a silly example. Who would let such an little thin get in the way of going to weekly meetings of atheists? Nobody I know, but then most of my vocal atheist friends I know through organizations that meet weekly.
I believe there is a whole collection of other examples of atheists stumbling over their own rhetoric.
Evangelism. We agree that evangelism is bad. What is bad about it? I consider it bad because it's done in socially awkward situations, and the views espoused are often offensive, wrong, and offensively wrong. But lots of atheists apparently think that trying to persuade people on religious topics is bad in general, and criticize other atheists as too evangelical.
Spirituality. Most atheists I know recognize that it is silly to let the lack of a spiritual realm get in the way of expressing awe, wonder, and other profound emotions. They do, however, see it as a good reason to not use the word "spirituality", since if spirits don't exist, that's not really what it is. I don't sympathize with the need for awe and wonder, but good for them for not letting any rhetoric prevent them from enjoying themselves!
Ritual. I quote PZ Myers: "Tapping into our psychology to get us to sit and get sucked into pointless ritual is not how I want to see the atheist movement evolve. I want us to think and act, not reassure ourselves by going through repetitive motions, through superstitious behavior." But then, I think lots of atheists are fans of Halloween, which is also filled with pointless rituals. (I don't particularly like Halloween.) What's that, some people enjoy Halloween? Who am I to begrudge that?
Priests. Obviously something has gone wrong with the Catholic priesthood, but what? Is it because any sort of leader or authority figure is bad? Is it because celibacy is unnatural? Surely we can think of a more nuanced reason that doesn't also apply to student group leaders, public intellectuals, or people who personally choose to remain celibate. How about... upholding a group as morally superior, to the point of concealing any evidence to the contrary?
Church. I must say that I completely agreed with PZ's title: "Atheist church? NO THANK YOU." I really hated church because it was boring. Also, I think church music is terrible. Yes, gospel music too. I think it is hypocritical that many atheists will say I'm letting my atheism get in the way of enjoying religious music (even though I also disliked it when I was religious), and simultaneously let their own atheism get in the way of recognizing the value of a church-like community structure. Are we incapable of seeing that different people have different tastes?
I certainly don't share the taste of atheists who feel the need for a humanist chaplaincy, but I don't see what is so wrong with that. People can do what they want, or not do what they don't want. People can also complain about other people's terrible taste. But let's not get completely carried away there.