The thing is, it's not wrong to say that pedophiles and such use reddit. They do, in the same way they use phones, TVs, and cars. It's not an apt description though, if someone asks you what reddit is, to talk about the racism and hate and what not. The reason being is that the bad stuff isn't the typical reddit experience and doesn't describe the whole thing well.
In Scott's post he gives the example of the Wizard of Oz review (girl goes to a surreal landscape, kills the first person she meets, then teams up with three strangers to kill again). Maybe it's technically true, but it's not an apt description. It doesn't really capture what the movie is like.
Where I'm going with this is: maybe you can find neo-reactionary or pro-eugenics or racist comments on the blog. I don't recall any examples of horrible comments from the NYT but maybe they are there. Maybe you can find a line or two, like the "feminists are Voldemort" that seem bad and worse outside of context. That's not really what the blog is about though and in a newspaper article describing it probably shouldn't zero in on minor blemishes or debatable flaws and use them as the main focus. Wasn't this supposed to be about Silicon Valley's Safe Space, or getting into the zeitgeist of the "rationalists"? How did the NYT article even attempt to do that? To my reading the NYT was just focused on complaining about the "problematic" aspects and nothing else.
I think it's fair to talk about problematic comments on a blog but it's not fair to act like problematic comments or loose associations to objectionable figured are the main thing when they really aren't.
Regarding your point about the feminists and Voldemort, if memory serves Scott was referring to a specific group of feminists and not likening all feminists to Voldemort. That's not really the impression I got from the NYT though.