I'm really not the kind of person who hates on Japan for no reason. I've been there, I used to study the language and culture full time. Most of my favourite films, authors and artists are Japanese.
But I have no problem saying that I see something fundamentally wrong with a culture where women would rather dress up as Coke machines than call the police, or where a major university can set up a fucking rape society to go around and gang-rape female students in the full knowledge that they will be too ashamed to even tell anyone. Of the sample of about 20 Japanese-born Japanese women I know, every single one has been sexually assaulted at some point in their lives. None of them even attempted to prosecute. It's likely none of them could have done.
It would be fantastic if all these things could be attributed to Otaku culture, but there are wider problems with the way most Japanese people deal with sexual politics and consent. Beyond that, homelessness, LGBT issues and mental health are, in my experience, treated with similar disregard or denial. There is a culture of silence and shame around these things which leads to real people on the ground being genuinely isolated, excluded and harmed.
Pointing that out is not being racist. Suggesting a correlation between that and the visual media is not racist. It's not like us enlightened Western folk do these things perfectly, of course, or can speak from a position of unqualified superiority, but cultural respect does not have to mean cultural relativism. There is no obligation to offer respect to the widespread acceptance of sexual violence simply because it's 'a part of Japanese culture'.
In short, while the visual media may be enjoyed by a relatively small proportion of the population, there's a reason it exists, and there's a reason it hasn't been curbstomped out of existence like it would if you tried to release similar things in most other developed countries.