One reason would be that the lower fertility rate is still high enough to keep the genetic material in the gene pool. Gays do reproduce, because so many of them try to be heterosexual first.
Personally, I am not all that impressed with the genetic evidence (although I would not rule it out completely). I think it is much more likely that the primary impact comes from a biological factor in the uterine environment. Natural selection would not eliminate this as those who have it are obviously reproducing. Supposedly there is now some evidence that women who have homosexual children are more fertile than those who do not, but I have not seen the data.
As I understand evolutionary theory, any genetic characteristic that results in a fertility rate of only 1% lower than that of other characteristics will eliminate itself from the gene pool within 1000 generations.
Fertility rate differentials greater than 1% will eliminate faster.
For example, sycle cell anemia, a known genetic defect, should have eliminated a long time ago but since it has some as yet unknown benefit(s) that that offset the expected negative impact on fertility rates, it still survives.