Bingowings said:

I remember there were jokes at the time about the jellyfish people being gays because they were both blue, now one of them is pink.

Star Trek is the most homophobic Science Fiction series on the planet.

If this is the best you can offer as evidence, I'm afraid I'll have to disagree. The episode The Outcast was nothing if not obviously supportive of gay rights. Perhaps there is more evidence you could provide to indicate otherwise, but it's always been a rather liberal show. The Original Series was pretty macho, so maybe that's what you refer to.

EDIT: Under background information in the link, it includes other episodes that address homosexuality as well. It also says that the Enterprise series did indeed arouse people's ire over homosexuality. Still, I think it is not a homophobic show in general.