“Christianity persecuted, tortured, and burned. Like a hound it tracked the very scent of heresy. It kindled wars, and nursed furious hatreds and ambitions. It sanctified, quite like Mohammedanism, extermination and tyranny . . . ”
— George Santayana, philosopher (1863-1952), Little Essays, No. 107, "Christian Morality"
It has become amazingly commonplace to hear or read of Christians accusing atheists of intolerance. This is nothing short of Kafkaesque. The majority of Christian churches still have intolerance as their official policy with regard to atheists and others. They have for centuries hunted us down like vermin for the pleasure of torturing us to death. Even now that they have been forced to give up that sport in most countries, they wax eloquent about their desire to see us burning in hell for eternity and about how much they will enjoy looking down from heaven to watch our torment.
For a theist to accuse an atheist of intolerance is the historical, logical, and moral equivalent of a Nazi accusing a Jew of intolerance. Any Christian who does so is a combination of insane and ignorant. Such a person simply is not in touch with reality and should be avoided because he or she is clearly able to delude himself into hating you for simply existing. There are many such people out there and their twisted way of rationalizing their insecurities into hatred can only be the product of religious education. A real education would have left them with some knowledge of the reality of the history of their religion as well as the difference between "disagreement" and "intolerance".
Tolerance means that a person can believe whatever he wants and the rest of us don't bother him about it, but it doesn't mean that the rest of us don't have a right to disagree and say so. The religious would have us believe that we are being intolerant of them simply for saying that we disagree. This is a clear case of psychological projection and an implicit threat. A person who can twist disagreement into intolerance can and will twist anything you say or do and use it as an excuse to try to bring harm to you.
A recent study, written about in this article, shows that even statements of the golden rule taken from other religions make the religious suddenly feel more intolerant rather than less. As the article correctly points out, this is proof that religion's appeal often lies with in-group versus out-group competition and dynamics.
I have had personal experience with such people. One cannot hope to sway them but pointing out the obvious absurdity of their statements and attitude can help to knock them off their moral high horse. Here are some of the things you might say. Generally, though, depending on the situation, you should immediately get away from such a person and never have any contact with him or her again.
"Disagreement is not the same as intolerance. Calling it that is clearly an example of psychological projection: You are simply accusing me of what you feel."
"Given your religion's centuries old tradition of seeking out and exterminating all atheists, for you to accuse me of intolerance is the historical, logical, and moral equivalent of a Nazi accusing a Jew of intolerance."
They will undoubtedly reply to this second suggested statement with accusations about how Stalin and Mao killed millions. You can reply:
"Stalin and Mao did not hunt down and exterminate every religious person they could find and they certainly didn't burn any of them at the stake. Most of their victims were political opponents or died as an unintended result of a radical switch to a new and non-functioning economic system."