This is a bit of a difficult one. Not being a homosexual male nor a fujoshi, I'm not qualified to comment on the preferences of either group. The entire Japanese department at my university is gay, and one of my teachers does a lot of research on various aspects of yaoi, and from what he has told me, it seems like it similar to any genre with a basis of sexuality. Some people read it for titillation, some for romance plots, some for story, and some read it because they can relate to the characters.
As for LGBT in Japan in general, while it is not "proper" to flaunt one's preferences, there is an overlaying idea of homogeneity in the Japanese community. Everyone is Yamato and heteronormative, and anyonewhosaysanythingelseiswrongsoshutup. This is, like any culture, just an over-lying view, and how liberal a person is depends greatly on the individual, or the area that you are in. Still, many gay Japanese men and women prefer to hide their preferences, because in companies or schools, individualism isn't appreciated, and could reflect badly on their social standing in either domain.
The reason that many people who are just realising their attraction to the same sex get confused about it is because homosexuality is not a widely discussed topic. My teacher once asked me if I thought that gay marriage was illegal or legal in Japan once, and knowing Japan, I said "illegal". Turns out that it was a trick question, and that gay marriage is not legislated at all! I believe that the confusion expressed by yaoi characters is reflective of the confusion caused to gays in Japan, who don't know that being gay is a "thing" (although, I think that them not more vehemently denying it is where the unrealism comes in).
Sorry that I rambled a bit, but this is the sort of thing that requires a thesis by a sociology major, and is not a very easy topic to cover in a paragraph or two!
