The idea of a gay gene (or more appropriately, gay allele) need not be treated as a binary concept: present and on, or absent and off. Instead, if someone has a gay allele, i.e. gay version, of a gene, then s/he might have a tendency to develop as homosexual. This might be involved with hormone cues (timing, dosage, etc.) that can affect brain development. Brain development, though, is a complex process and heavily influenced by enivornmental variables as well.
Therefore, homosexuality having a genetic component does not negate environmental influences. This means that a gay allele can be fairly neutral, overall, towards the evolutionary fitness of the organism in hand.