Sorry to be anal but atheism isn't an organised group.
Neither Christianism, Hinduism, Agnosticism, etc.
For each self-distinction made amongst human groups (whatever their validity), you would found an organized body if you have a large enough definition, or no one with a really narrow one.
Let me propose mine : an organised body, is one agreeing on a (strict or not) hierarchic organisation unifing whole the social group. It means you can have atheists groups with a diverse degree of unification and cohesion, or religious groups with the same.
Of course, religious bodies having a more long history of social organisation, they had also more time to commit persecution of their own, or to prevent them.
So, yes, you had groups that, by arguing of an atheist or anti-clerical necessity, that actively participated or launched anti-religious persecutions.
Atheist doesn't mean you can't be an intolerent dick.
Some of the historical examples given of "persecution by atheists" usually are based on communist regimes but considering many of them had state controlled churches and went after other non-religious groups, this was more a question of preventing parallel power structures then persecution targeted at religions.
So your point is as long non-religious persecution affects only some religion, it's not the same than inter-religious persecutions?
Allow me to disagree. It's not because you have puppets bodies that it means other, less fortunates bodies aren't repressed for religious reasons : Uniates, for instance, weren't repressed on the policy of their church, or ethnic grounds, but because their were Uniates, period.
That their motives cover or are in parallel with other ones, I agree with you : it's also the case for the extremly massive majority of religious persecutions (some random exemples : persecution of Druidism in hope of destructucrate celtic polities, persecution of protestantism in France in the same time of political civil war motives, fitna on Arabo-Islamic world on dynastic and religious grounds).
