You won't likely see any of this, but I've had many conversations with Japanese and this subject, and their views are often strange, misguided, and quite negative in regards to homosexuality they just don't get it.
Many Japanese see homosexuality as predominantly foreign, so for some of them, seeing gay Westerners be a somewhat unsurprising confirmation that Westerners are sexually promiscuous/immoral/below the Japanese. Once again, as the above poster mentions, Japanese people generally dislike PDA, and homosexual PDA will draw even more attention, and people will definitely be talking among themselves about it. Particularly in minshuku, which are owned by individuals, you may want to (or have to) sleep as straight men, depending on how the accommodations are set up. The Japanese are 'tolerant' of homosexuals in the way that you should not be harrassed by others HOWEVER, they are generally not tolerant in terms of accepting homosexuality. As the above person said, gay couples can feel quite safe in Japan.