Ehh, the anime industry makes me think it's more a majority. The otaku culture is pretty prevalent in Japan.
Not quite.
Otaku can be looked down upon in Japan as much as they are in the West, if not more.
However, I should note that, whereas we Westerners use the word "otaku" to describe hardcore/obsessive fans of Japanese media, the word "otaku" has a slightly different meaning over there: it means someone obsessed with a particular interest, not just anime. I remember reading something about Iwata in which claimed that he "would be considered an otaku nowadays" (due to his passionate interest in programming and software design).
Basically a more equivalent term to us would be nerd or geek. (Tagging
@PushDustIn here for some input.)
However, you could say the percentage of (anime/manga/video game) otaku in Japan is bigger than in the West for higher exposure. They're a bigger minority, but still a minority. Nevertheless, it's significant enough so that companies can exclusively exclusively target that niche and secure an audience.
Of note is that people of all ages in Japan read manga, so it's not a niche market over there. There's all sorts of manga spanning multiple literary genres with different degrees of maturity and art styles. There are even manga series aimed at elderly people!
AFAIK, I think that anime doesn't have the same kind of broad appeal as manga, being more primarily aimed at younger audiences, but there's animation targeted at older and niche audiences, usually broadcast at late night and/or on less accessible TV channels (satellite and such).
After months of waiting, my NeoGaf accounted got validated, so now I can post there. :D
Let's see how long will you last, then.