It is indeed. But atheists have a tendency to think it’s fine for them to be hateful towards religious people because “they hate all religion”. Logically hating more people makes someone even worse, but there’s not all that much logic going on in the minds of some atheists. For some people, Atheism is just a cover for being hateful, in exactly the same way some people use Christianity (or any other religion) to provide cover for their hatred.
If the guy didn’t say something about “deists,” the comment would be identical to something an Islamophobic Christian might say. Religious bigotry from atheists is identical to bigotry coming from religious people.