Gallup explains the difference may be explained:
The under-representation of LGBT Americans in the ranks of the religious in the U.S. today has a number of possible causes. Some of these center on the effect of church policies and doctrine, which have historically been disapproving of non-heterosexual love and relations, while others may reflect demographic and geographic differences in the LGBT population compared with the rest of the population.
Societal attitudes toward same-sex relations have become more accepting, and recent stances taken by several churches and religions reflect this. Just this summer, the Presbyterian Church (USA) voted to allow that denomination's ministers to perform same-sex marriages in states where it is legal. If these types of shifts continue, LGBT adults may be more likely to feel welcome in attending churches and other religious institutions, as well as in identifying as religious, personally.So maybe that's why atheism and gayness go together like rainbow flags and pride parades!