Let's start this out with what's happened in the Catholic Church. The Catholic Church had a problem with pedophilia. That can be expected, after all Catholics are made up of the general population, and some people happen to be pedophiles. It's bound to happen in any large organization. What's important is how the organization deals with the problem.
They need to treat it like a problem: they need to report the problem to proper authorities, shame the offenders in their own community, apologize deeply to the victims, and put protective systems in place to ensure that the problem doesn't happen again in the future.
That didn't happen. What did happen was that they denied a problem, labeled it a PR problem, and tried their best to sweep it under the rug, ignore it, or blame the victims. They excused the offenders and enabled them and their anonymity by shuffling them around and did everything possible to deny that anything was a problem. When it erupted to the surface, they had to take different tactics, still just as slimy. They complained about being unfairly yolked with the blame. They did everything but address the issue and ensure that it wouldn't happen again in the future.
And that sort of response is the kind of response that I'm seeing in response to sexism within the atheist community. The atheist community has been having a problem with misogyny. And that's to be expected. After all, atheists are made of people, and some people can be misogynistic. The important thing is looking at how atheists deal with the problem. Unfortunately, there's been denial of a problem, blaming the victim, fervent apathy towards admonishing people on the internet, misguided attempts at defending free speech, and complaints about being unfairly yolked with the actual perps.
And those are all the wrong reactions. When someone in your group does something bad, the group need to react with unity in correcting the behavior. At the very least, individuals need to not interfere with those who are doing the right thing. Because otherwise it's just enabling the problem to continue. It's saying that we're okay with the status quo. We shouldn't be.