Apparently Kristof was responding to the increasing criticism of religion by people like Sam Harris and Richard Dawkins (see the Beyondbelief2006 website) and pleading for tolerance.
Harris and Dawkins responded to Kristof's column with letters to the Times. Here is Dawkins' letter.
Nicholas D. Kristof is one of many commentators to find the tone of the newly resurgent atheism “obnoxious” or “mean.”It seems to me that Dawkins and Kristof are deliberately not talking to each other. In my opinion, Dawkins is right that religion is wrong when it makes claims about the physical world. He is right in criticising those claims. And he is right that for the most part the criticisms of those claims are stated in relatively moderate tones. It's so easy to make the case that religion is wrong about the physical world it can be made in very moderate tones. These are very easy points to score.
Ubiquitous as they are, such epithets are not borne out by an objective reading of the works he cites: Sam Harris’s “Letter to a Christian Nation,” my own “God Delusion” and www.whydoesgodhateamputees.com (I had not been aware of this splendid Web site; thank you, Mr. Kristof).
I have scanned all three atheist sources carefully for polemic, and my honest judgment is that they are gentle by the standards of normal political commentary, say, or the standards of theater and arts critics.
Mr. Kristof has simply become acclimatized to the convention that you can criticize anything else but you mustn’t criticize religion. Ears calibrated to this norm will hear gentle criticism of religion as intemperate, and robust criticism as obnoxious. Without wishing to offend, I want “The God Delusion” to raise our consciousness of this weird double standard.
How did religion acquire its extraordinary immunity against normal levels of criticism?
Kristof is right that most religious people are not religious because of the claims religion makes about the physical world. They are religious because they value the perspective religion provides on subjective experience and on questions related to subjective experience such as "What is a good life?" and "How can I come to terms with death?". Kristof is right that a failure to respect how people deal with such personal and fundamental questions can seem intolerant no matter how gently that lack of respect is expressed.
This entire controversy could be settled if religion would forswear making claims about physical reality and if the critics of religion would recognize that the value religion has for most people has little to do with those claims — even if many defenders of religion don't realize this. But both sides seem to be too stubborn for something so simple.