There are examples of atheist fundamentalism persecuting religious believers; I've seen this in my own life, so don't tell me it never happens! This still goes on; in some countries priests still have to operate in secret or suffer imprisonment, even death.
Yes, fundamentalism is bad. I'm sure many horrible things have been done in the name of atheism, just like most -isms. It's something that needs to be avoided.
BUT! The important point to make is that their is nothing intrinsic in the doctrine of atheism that dictates that atheists should kill non-atheists. Any crimes that come about in the name of atheism
do not come out of atheism, but come out of other beliefs of the criminal. Saying, "I'm going to kill you because atheism says I should" doesn't make it so. If you do not believe in God, it does not logically follow that you should murder those who do not.
The issue most atheists have with religion (not all religions, but most of the big ones) is that they
do have explicit doctrines that dictate that the believers should convert or kill the non-believers. Saying, "I'm going to kill you because the Bible says I should"
does make sense when a.) you believe in God, b.) you believe that the Bible is God's word, and c.) the Bible does in fact tell you to kill non-believers.
Deuteronomy 17
17:2 If there be found among you, within any of thy gates which the LORD thy God giveth thee, man or woman, that hath wrought wickedness in the sight of the LORD thy God, in transgressing his covenant; 17:3 And hath gone and
served other gods, and worshipped them, either the sun, or moon, or any of the host of heaven, which I have not commanded; 17:4 And it be told thee, and thou hast heard of it, and enquired diligently, and, behold, it be true, and the thing certain, that such abomination is wrought in Israel; 17:5 Then shalt thou bring forth that man or that woman, which have committed that wicked thing, unto thy gates, even that man or that woman, and shalt
stone them with stones, till they die.