As a gay man in Japan, I have some experience in this, so let me give my 2 yen. First, there is no religious bias from most Japanese. Historically, many Japanese have been homosexual (some buddhist temples in Japan actually kept young men {even young boys at time, sadly} specifically because they were beautiful and the monks would have regular sexual encounters with them, and samurai often had relationships with their "squires" or "apprentices" {not sure what the Japanese word for that is} )according to some of the gay literature I have read here.
That said, there is a strong bias, not against same sex acts, but against a homosexual lifestyle, because it is not within the traditional Japanese lifestyle. A youth is expected to go to school, get a job, get married, have kids, and support the family by doing so. Someone who falls outside of that pattern is instantly regarded with suspicion and even contempt by many traditional Japanese. Obviously, a homosexual relationship and lifestyle falls well outside that pattern.
I would liken Japanese homosexual culture to that of America in the early 70's, without the active persecution or violence of that time. Most people don't even consider it (you'd be AMAZED how many Japanese have told me that there are no gay Japanese...hand to god!) Those that do, often consider it a choice (and not a good one) and somehow deficient, although many women do consider it hip and cool to have a gay male friend. There is a lot of confusion, incidentally, even in the language, about the difference between being gay, trangendered and transvestite. In fact, most words in the Japanese language make no distinction between the different identities. Ironically, while homosexuality as a lifestyle is looked at askance, entertainers who break the gender boundaries are incredibly popular, both as objects of amusement and as legitimate entertainers.
This leads to many Japanese having confusion about or denial of their orientation. The Japanese closet is deep. Almost all the gay Japanese men I have met over 30 are also married with children. Many of their wives even know that they are gay. It seems that as long as they have fulfilled the obligation to the community of a wife and children, it is tolerated. Some just look at it as a physical thing (and the stereotype is that this sort of Japanese man is very unaffectionate with their partners in gay sex; no kissing or any form of emotional attachment is formed); that they simply want sex with a man as an urge to be satisfied. This attitude is also held by many heterosexual Japanese about homosexuals, that it is simply a physical urge, not a life-altering orientation.
Many other gay Japanese men go the far opposite extreme, becoming extremely effeminate in all their behavior; sometimes even dressing and appearing as women (although not quite to the degree of transvestism). Rather than hiding it, they embrace the stereotype that Japanese culture places on them and in fact seem to be throwing it back in that culture's face.
Gay bars and gay-oriented businesses are few and far between outside of the metropolises (such as Tokyo's Shinjuku Nichome) and compared to the America, even those venues are small. For instance, Nichome has approximately 200 gay bars (according to Fodor's) in the neighborhood, but from personal experience I can tell you that aside from a very few, these bars have a seating capacity of 6-15 people...they are bars, not clubs. There are also occasionally places in the most out-of-the-way towns that would shock you...my small town does not have a gay bar (or in fact any night clubs) but it does have a transexual snack/hostess bar! HOW it stays open in this town, I couldn't even tell you...
There are quite a few small gay newspapers and magazines published in Japan, and they tend to be very discrete in delivery. In the larger cities, there are gay encounter/social groups as well.
Now, a bit of good news for foreigners coming to Japan...usually, Japanese have NO problem with homosexual foreigners. Remember, we are expected to not conform to Japanese culture (which can work for and against us in many situations) and so without any religious bias against homosexuality, we slip unscathed under the "conformity" radar...it's just one more weird thing about you, like eating raw vegetables, hating natto and wearing non-white shirts to work.
However, there seems to be a bit of mild prejudice about us working with kids (or maybe not...I'll explain). A few of the teachers I work/have worked with who know my orientation have told me it would be better for me not to talk about it, as some parents might be uncomfortable with me being in charge of their kids. On the other hand, several of my gay JET friends are not only out at the schools they teach at, but they have even taught lessons on homosexuality in other countries and how it is received there, without any negative fallout. So it could be that the teachers who spoke to me were simply being extra cautious, or my friends could have been lucky.
I hope this is useful to you, or at least informative.
Sean