This may go without saying, but the West's biggest issue with homosexuality is religion, since all of the Abrahamic faiths (Christianity, Judaism, Islam) condemn it. In Japan, it's more of a sociological issue...
Well, considering the fact that Christians invaded Japan as well as many other nations, Shinto and Buddhism has adopted many of the Christian ideas. Before they invaded Japan, homosexuality was something that was accepted to be natural, and not a big deal. Another reason Japan finds it hard to accept gays is that under-population there is really, really bad.Even though some understand that the reason Japan is under-populated is because the men are at work all day, and women are expected to keep house, resulting in less happy time, people still blame gay people.