I don't seem to find it particularly appropriate or odd, actually. It's purely the result of who wanted it to happen, and where they happened to live. There happens to be a large base of anime/manga fans in the Bay Area, anyway. It's coincidental that the convention happens to be happening in what is probably the most liberal city in the most liberal state in the nation, one that happens to have a reputation for being relatively tolerant of homosexuality.
Of course, my real question is what was the point of making such an observation in the first place. This has really nothing to do with the subject of cosplay at Yaoi-con at all.