Almost certainly. Not that there are no homophobic atheists, but major religions like Xtianity and Islam (even some types of Buddhism) have tenets that oppose it, which encourage people who otherwise wouldn't care about homosexuality to oppose it. A lot of religious people, at least in the West, sort of want to be non-homophobic, but feel compelled to oppose homosexual behavior because of their faith. When you don't have religious reasons to oppose it, it becomes more of a "who cares" for most people.
If no religious condemned homosexuality you'd probably see an equal number of religious and irrelgious homophobes.
If no religious condemned homosexuality you'd probably see an equal number of religious and irrelgious homophobes.