That article paints an IMHO unrealistic picture of the acceptance or even visibility of homosexuality in Japan. There are a few celebrities who are openly gay, but most Japanese people don’t personally know any “out” homosexuals. There’s not even much of a gay club scene outside Tokyo and Osaka. When I lived in Japan I was told more than once that until relatively recently (the past 50-100 years) there were no homosexuals in Japan at all. The fact that there are gay Japanese people now is attributed largely to foreign influence.
In my experience the Japanese do not consider homosexuality to be sinful or immoral, but many think of it as being unnatural, disgusting, or just plain weird. It’s somewhat similar to how people who are into S&M or have sexual fetishes are regarded in the US – as long as everything is consensual then most other people don’t have any interest in preventing these non-mainstream sexual behaviors, but they find the subject at best embarrassing and would generally prefer not to hear about it. The big exception is some women who (thanks largely to Sex & The City) think it would be nice to have a gay guy as a friend to go shopping with. Several women told me they’d like to have such a friend, but admitted there was little chance they’d ever meet such a fellow unless they went to Tokyo or Osaka first.
What seems to throw off a lot of Westerners is that the Japanese consider same-sex crushes among adolescents, especially those in single-sex schools, to be fairly normal…as a phase. Kids are expected to grow out of this by high school age. Where I think Japan is considerably ahead of the US is in acceptance of transgendered people, but that’s really a different subject.
ETA: I should qualify this by saying I haven’t lived in Japan since 2004, so it’s possible things have changed a lot since then. But that’s not my impression based on the Japanese friends I’m in touch with or the Japanese exchange students I’ve met since 2004.