Not unless you assume atheism somehow implies support for gay rights. It doesn't. There are many atheists who are intolerant of gays. Far more religious people, sure, but not all discrimination against gays comes from a place of religious devotion.

Half the people who go gay bashing aren't what you'd call religious scholars or even devout practitioners.

A lot of anti-gay sentiment is generated from a fear of that which is different. A lot of people find it "gross" or "disgusting" because they can't step outside their own boxes. Religion reinforces these feelings, but it's not solely responsible for their existence.

EDIT: I'd also point out that religion is not the cause of homophobia, but rather religion is used as a convenient excuse to codify pre-existing homophobic tendencies.

Homophobia existed before "religion" as we understand it today. It didn't come from religion, but was rather excused by it.

On a very basic level, there is nothing about the concept "God exists" that logically leads to "homosexuality is morally wrong."

Religion has been used to dogmatize and insist upon these prejudices, sure, but are not they product of theism. Rather theism has just been used as a convenient excuse to indulge in prejudice.