I know this thread's been dead for a while, but I just want to say...
Just because there are some gay characters in science fiction, it doesn't mean that there isn't a problem with homophobia. I've found it extremely difficult to find science fiction with LGBT characters, and even harder to find science fiction with LGBT characters portrayed well and realistically.
I actually prefer stories and books about straight people, because I have trouble identifying with lesbians as they're presented in most literature. A gay character can't just be a person who happens to be gay. In literature, there always has to be a reason that a girl "turned" gay, like she was raped or abused or some other tired old cliche. Lesbians are often oversexualized and undercharacterized in the media, portrayed as predatory and, almost always, as feminine. I'm a socially awkward genderqueer geek gay. I can't relate to that.
I can't relate to the omnisexual/pansexual trend either, and I suspect it's because most omnisexual/pansexual characters are written by women whose sexuality is leaning towards the straight side of the spectrum. Women who think, "Hey, it might be fun to have sex with another woman," but who have never truly had feelings for a girl and for some reason are incapable of imagining it.
People forget that "homosexuality" isn't just about sex. I don't care how "progressive" sex scenes become in science fiction. I don't much care for erotica or romance, be it straight or gay. What I think is lacking in every genre of fiction is believable, strong, interesting characters who happen to be LGBT.
I know such fiction exists, but I haven't been able to find much of it.