In what context are you asking this question? Western European social democracies? Coastal urban centres in the US?

Certainly there are vast portions of the world today where this statement is demonstrably false. The US Congress has zero (publically) atheist members, and atheism is more of a negative trait for US politicians than being gay or Muslim.

Many Islamic countries either explicitly or via anti-blasphemy laws make atheism illegal, with punishments up to and including the death penalty.

I'd suggest something more along the line of "What were the origins of the social stigma against atheism in (whatever culture you meant)?" I'd certainly be curious to know what impact anti-Soviet sentiment had on this during the Cold War.