the problem is ignorance, not intolerance
Vjack at Atheist Revolution has a great post on “Religious Intolerance” that opens with this:
From a Christian perspective, spotting religious intolerance is a fairly simple matter. Odds are, if you are an atheist, you are intolerant. And yet, this is a simplicity based on irrationality and Christian privilege. What is religious intolerance, how should we recognize it, and is it a crime of which all atheists are guilty?
While the accusation of “intolerance” is often made against atheists, it is supported only anecdotally. The data actually support the opposite conclusion: freethinkers (atheists and—particularly—agnostics) are far more tolerant than theists. Bruce E. Hunsberger and Bob Altemeyer, demonstrate this in their book Atheists: A Groundbreaking Study of America's Nonbelievers:
Agnostics almost always had the lowest scores on dogmatism, zealotry, and religious prejudice; and atheists usually placed second, while the inactive believers usually scored higher than any of the nonbelievers, and the high fundamentalists towered over everyone. (p. 122)Nonbelievers, including the atheists, usually proved less dogmatic, less zealous, less authoritarian, and less prejudiced than any of the believer groups, even the relatively low-scoring inactive believers. (p. 128)
Vjack makes a similar observation:
I think it is fair to say that I have never met an atheist (nor am I such an atheist) who does [not] agree that others have a fundamental right to hold any religious belief they select. It is your absolute right to maintain your Christian beliefs even if they are false and even if they cause harm to you. I hope you will outgrow them. I think they are laughably absurd. I have not one shred of respect for the beliefs themselves. However, I respect and defend your right to hold them.