Atheist societies promoting homophobia or discrimination...

My two cents: While religion and machism may play a big role in homophobia and sexism, I believe that discrimination is mostly prevalent in societies and groups that have a strong desire to separate from other groups; or in other words, a strong "us vs. them" mentality.

These groups tend to not accept the unknown, or differences. They also might consider strength and combativity as virtues, which brings us to machismo.

Whether the rallying point is a religion, or nationalism, or class combat, is not really important. But I believe it's not a coincidence that the more inclusive and less against other religions a faith or religion is, the more likely it is to not be homophobic.