I'm the type that makes people uncomfortable.
I feel bad, because on the one hand it sucks that Japan is so conservative with LGBT issues compared to many of its allies, but on the other hand I love the dorama that it brings.
Actually Japan was never against LGBT people. After the Americans took over that stigma was created. Japan is also one of the most accepting country's in sex or kings.
Its actually a fair bit more complex than that and to say homophobia in Japan was a creation Americans or Westerners in general is complete bullshit barely worthy of a response.
See, the Japanese tend to only be accepting of same sex encounters, not relationships. Japan is supremely conservative and has very strict gender roles, so while a fling or a teenage relationship might be acceptable, serious relationships are not and attempting to maintain a same-sex relationship beyond your youth is viewed as childish and something that you need to be "cured" of.
A strong emphasis on marrying and producing children only furthers this distaste for homosexuality and adds a layer of discomfort for asexuals as well
Said conservatism towards gender role also means transsexuals are right out. Hell even tomboyishness is often viewed as freaky or unusual, enough that tomboys, no matter how good looking, nice or all around wonderful human beings they may be, are frequently viewed as undesirable and odd for not conforming.
Non of this has anything to do with Americans or westerners in general. All of this has been a part of Japanese culture for hundreds of years, which is why it is so hard to get the Japanese population as a whole to change, cause unlike in the US, where the core of reactionary homophobic movements is often (but not always) some sort religious fundamentalism dogma, in Japan it is simply the way things are. Its not some small but vocal group who want to "kill all the queers" but is a universal and accepted idea homosexuality is simply a phase that is grown out of and if not, then it should be cured, because in Japan men act one way and women act another and deviating in any way from this is grounds for punishment or at the very least "justifiable" discrimination.
TL;DR Japan isn't "not homophobic" and "not conservative" and homophobia is not something that Japan imported from the west.