To expand, yes there have been some specific instances where atheists have taken the rights of theists away.
The USSR’s anti-religion campaign had a destruction of the Church, this was due to the Church’s support for the status quo. We demonise the communists but forget that the people they were overthrowing were as brutal and more callous. Russia was in a WW I, famine was massive and the ruling class was effectively splurging money on themselves. Royal families that separated themselves and maintained their lifestyle during a national crisis tended to stop being Royal quickly and this was no different. But again, this was not due to atheism, this was due to the political stance of the Church. Had the Church remained neutral it would have survived.
China’s anti-Tibet campaign has specifically targeted Buddhist Monks due to cultural differences, but this is more due to the Maoist idea of cultural unification rather than atheism in particular.
The most violent one was the Cult of Reason during the reign of terror. Which was built on atheist and pagan principles that “worshipped reason”. And yet again the core of the hate was the Catholic Church’s propping up of the French Aristocracy that was (again) woefully out of touch with the public and treated the famine as a joke.
Another weird example is the deist “Cult of the Supreme Being”, another French Revolution incident. This one is interesting since it is a deist fundamentalist movement.
Many of these were run by atheists and some of the reasons were to “create a secular/atheist state”, but all targeted religion because it was the tool of an oppressive state. We know of the famines of the USSR since the USSR kept records, those famines were the norm pre-USSR too. The difference is that no one cared about starving peasants, famine was rife but since no one really bothered, no one kept records of dying poor people. With the rise of Communist theory, the workers quickly recognised that they were “being had” since there was no reason to keep the useless nobles who effectively “wasted” food. They were good for fighting? We only thought like that because nobility was an entrance to being an officer and the Crimean and WW I taught us that the best officers were people who knew to be officers rather than some chinless wonder getting by on his surname. We all learnt lessons from the Communists.
Including our Royalty…
During WW I the British Royals did not flee from the bombing raids, which helped cement their reputation since they specifically mentioned “the people”. They also cut down on rations and gave away food. During WW II, they actively served in the army. The future Queen of England working as a driver of a truck. She saw active service in the UK as an auxillary. Many served overseas. Prince Harry serving in Afghanistan is not something novel, neither is Prince William being in the Coastguard.
The thing is we have grown since then. We recognise the mistakes of the Cult of Reason and police ourselves vigorously. We wish for a world without the pacifier of religion and superstition but we do not think murdering priests is going to solve anything. It will merely turn us into that which we despise.
None of these things were done because there are no gods but because of political and social ill will to religious groups.