New York Times: Sniffing Out the Gay Gene: The differences in the way that gay and straight men's brains respond to pheromones does not, by itself, prove that homosexuality is innate.
Homosexuality is a puzzle for biology, not because homosexuality itself is evolutionarily maladaptive (though no more so than any other sexual act that does not result in conception), but because any genetic tendency to avoid heterosexual opportunities should have been selected out long ago. Perhaps 'gay genes' have some other compensating advantage, like enhancing fertility, when they are carried by women. Perhaps the environments that set off homosexuality today didn't exist while our genes were being selected. Or perhaps the main cause is biological yet not directly genetic, like differences in hormones or antibodies that affect the fetus while it is developing.
Just as puzzling is the existence of homophobia. Why didn't evolution shape straight men to react to their gay fellows by thinking: 'Great! More women for me!' Probably the answer lies in a cross-wiring between our senses of morality and disgust. People often confuse their own revulsion with objective sinfulness, as when they dehumanize people living in squalor or, in the other direction, engage in religious rituals of cleanliness and purification. An impulse to avoid homosexual contact may blur into an impulse to condemn homosexuality.