It could work like that (though there were no conversion here). This kind of mob mentality can and do manifest itself over other channels than religion of course, but I think atheism is a less likely channel than religion itself.

Religion generally comes with a moral system, backed up by a set of beliefs. Among them, the belief that it is proper and good to believe (and, well, you know). It also comes with community by default, which can have a strong effect (compare r/atheism and r/religion: the more united tribe (atheists) sound much less tolerant overall).

The reason why someone turned to atheism may also influence his likelihood of persecuting believers. A Lukeprog scenario isn't likely to result in intolerance, for instance. Raw rebellion, followed by a "this is all bullshit anyway" rationalization may. I'd put being raised by atheists parents between the two, though it depends on the parents.

Anyway, I think the strongest factor is mob mentality. A group of anything that doesn't identify itself as such isn't very likely to make others miserable because of that "anything". And more often than not, atheists form such a group.