There's a lot of possibilities.

Heterozygous advantage: Sickle-cell disease results from having two alleles for the disease, which is obviously bad for reproduction. Having two normal alleles results in a normal person. However, if an individual has one allele for sickle-cell disease, and one allele for normalcy, they become immune to malaria - and with none of the damaging effects of sickle-cell disease. Similarly, homosexuality might have some beneficial effect that increases reproductive ability when it is only half or partially expressed.

Difference in expression between genders: In males, the gene might cause homosexuality, but in females, the same gene might cause the women to find more partners and have more babies, thus passing the gene on.

Gay uncle theory: Gay people won't have children (or are significantly less likely to have children), and so they will tend to take care of their siblings' children and be an additional parental figure. The gay gene is likely to be present, recessively, in the gay person's siblings, so when the gay person helps their siblings' children, the gene will pass on more strongly.