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I dont think new atheism proponents like Dawkins and hitchens propose religious persecution like communists.

Looking for social change towards atheism, like a third-wave atheism is very different from imposing atheism on people.

They don't propose it explicitly, they just lead people to it. Once you have started believing that religion is the root of all evil, you do not have to travel very far at all to find yourself persecuting the religious. The position they espouse isn't just a serious logical mistake, it is a terrible moral one.

Then you also lead people to theocracy.

There are positions one can take between "all religions are peaceful, good, and true", and "kill the religious"

You don't lead people to theocracy by warning against killing for dogma. On the other hand, creating dogmas about religion being the source of all evil can have pretty awful consequences.

There isn't a simple road between the two positions you gave, there is an entire territory.

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