I haven’t read the “angry atheists” comments in the Guardian, so I can’t comment as to wether they appreciate context or not. However I was struck by Andrews comment:

So when our readers claim that atheists never persecute believers, this is in part an absolute ignorance of some of the basic facts of twentieth century history — what did they think was happening in Poland up until 1989? — an in part a simple reluctance to believe that history is about other people. I haven’t shot any priests, and nor has anyone I know. Ergo, atheists never persecute.

This is a gross misinterpretation and over simplification of “the basic facts of twentieth century history”. And by taking a purely literal interpretation of the atheist’s statement “atheists never persecute believers” he is, I suspect, making a disingenuous argument.

Andrew’s argument goes something like this:

1. Fundamental Atheist’s claim: “atheists never persecute believers”
2. Marxist Communist are atheists
3. Under Communism religious believers were persecuted
4. Therefore the atheist’s claim in 1 is false.

However, if the comments could be read in context, I suspect that the atheist’s were actually trying to claim that “non belief” (i.e. atheism) has no propensity to encourage the persecution of people precisely because atheists have no beliefs to try and impose. In the historical context a better interpretation is that it was the need to impose the wider fundamentalist beliefs of Marxism and Socialism that led to the prosecution many groups of people; of which believers were but one.

When looked at in this context Andrews argument is clearly illegitimate.