Suppose there is a religion that says kill unbelievers. Let us say atheists find this repugnant and try to stop it. The members of that religion will cry persecution. But is it? Whenever you point to examples of atheists oppressing religion, it is mostly a reaction to the atrocities committed by said religion (and not some grand conspiracy on the part of atheists to wipe out religion. It is more a self-defense mechanism than an aggressive policy).
There are not many religions that say to kill unbelievers, first of all. Can you name a major religion that actually says this?
At various times there have been policies in the Church to persecute those who in some way stand against it. It is not usually such a blanket statement as "kill unbelievers". And often that was an excuse used for other things people in power wanted to accomplish.
I do not know how any adult can read history and think that those who tried to exterminate religion are somehow more innocent of persecution of anyone else.
Lets give another scenario. Say you have a set of beliefs that says "kill anyone who stands against us". This is an atheist worldview, as it happens. They do, in fact, systematically kill millions who stand against them, including those who oppose their power, who stand up for justice, and stand up for religion. (This is a real example in case you haven't cottoned on to that yet.)
Of course the Church opposes them, and tries to stop it. Is that really persecution?
No,
its not persecution to say it should be stopped or even to look for legal justice. And guess what, the Church in the particular instance I am talking about did not say they ought to be killed, or tortured, or anything of the sort. (Of course, they were never actually in a position to do so, they themselves were the ones being murdered and tortured.) But when that regime fell, they still did not advocate persecuting those who were a part of it. Nor did they advocate making their atheist views illegal or something that could not be suppressed publicly.
If they had advocated murder, hunting people down, and trying to suppress their atheist worldview, that would be persecution.
Your dichotomy between the acts of religious groups and non-religious groups is simply false, and history shows it amply. There have been organized atheist groups where atheism is an essential part of their philosophy, who have actively persecuted religion, tried to suppress even its expression and have treated members brutally.
It really makes me angry that people will not even bother to read history.
As for Dawkins - is he persecuting anyone? I think that is too strong a word. But he sure isn't respectful to others.