Atheists who argue that theism is unreasonable or irrational are being intolerant of theists. Atheists who argue that religion does more harm than good and/or is irrational and unreasonable are being intolerant of religious believers.. Intolerant, militant atheism is on the rise and is just like violent religious extremism.
There are several myths here, all tightly intertwined for the apparent purpose of getting atheists to cease making uncomfortable and unwelcome criticisms of religion and theism. Religious believers, mostly Christians, are responding to atheistic critiques of religion by claiming that vocal, unapologetic atheists are analogous to religious terrorists and that criticism of religion is a form of religious intolerance. The implication is that believers shouldn't have to be faced with criticism.
Examples of these attacks on atheists who dare to criticize theism and religion abound even, or perhaps especially, in mainstream media. Christian author Os Guinness has expressed hope for a "respectful exchange of ideas somewhere between the militant extremes of religious violence and militant atheism."
Robert Wright, a visiting lecturer at Princeton, has said that atheists who criticize religion may "undercut the very thing that makes America work as a civil society" and that Americans "restrain ourselves from saying bad things about religion, from talking about it at the dinner table. These guys want to talk about religion at the dinner table." Among the worst is Nicholas Kristof, a columnist for The New York Times, who has written that "the tone of this Charge of the Atheist Brigade is often just as intolerant and mean. Its contemptuous and even ...a bit fundamentalist."
Note how Guinness contrasts "religious violence" and "militant atheism" as if they were opposites on the same spectrum. This is a reprehensible distortion of reality because there is nothing comparable between religious believers who are willing and able to justify torture, mass murder, and terrorism on the basis for their religion; and are atheists who use harsh words, pointed criticism, and sometimes even mockery to make their case against religion.
Assuming that such people are sincere in thinking that a comparison can be made, they may fear atheists' criticisms as if they were an act of violence against their beliefs. This would indicate how much they fear criticism: serious, sustained criticism of the reasonableness of religious and theistic beliefs may be perceived as being likely to destroy those beliefs, just as violent religious terrorists destroy buildings. In other words, atheistic criticism of religion is feared as being too strong and successful.
More common is to call atheism "intolerant" when atheists criticize religious and theistic beliefs. People are upset that atheists don't treat religion with the sort of respect, deference, and honor which religious believers do. Robert Wright, for example, claims that we shouldn't say bad things about religion. Nicholas Kristof says that atheists are "mean" and "intolerant" for having the gall to say that there is no good reason for theism and that religion is harmful.
Instead of saying such mean and intolerant things, atheists are supposed to be respectful of and deferential towards religion, exactly what religious believers want and exactly what would give the impression that religion and theism are inherently good, positive, and worthy of belief. This means that people want to completely undercut atheists' critiques by portraying them as inherently unreasonable.
You won't find these same people raising the same arguments in other areas of disagreement, like politics. Kristof doesn't accuse Republicans of being mean or intolerant in their attacks on liberalism. Kristof doesn't object to movie and theater reviews in his own newspaper which are no less pointed and harsh than things which atheists say about theism and religion. These people also don't object when atheists themselves are accused of having no reason to be moral or when atheism is accused of being the cause of the 20th century's worst mass murders; on the contrary such people (including Kristof) repeat this charges as if they were self-evidently true.
They want to prevent these critiques from ever being aired by portraying them as contrary to whatever "makes America work as a civil society." Since when has America required people to hush up criticism of powerful traditions or institutions? Atheists in America represent a specter of doubt, questioning, skepticism, criticism, and even blasphemy. Irreligious atheists are like metaphysical anarchists who do not submit to the authority of any religious institution, not even those of "false" religions, and thus feel free to criticize all religions. Irreligious atheists call into question the validity of religion generally by merely existing. By living, and worse yet by living well, they demonstrate the irrelevancy of religion to having a good life.
When we atheists have the gall to speak out and actually say what we think, a bad situation becomes intolerable. People like Kristof and Wright don't offer substantive counter-arguments to atheists' critiques of religion and theism because they have none to offer. The best they can do is cry that the critiques shouldn't be raised to begin with. They can't say that openly because they recognize that this is genuine intolerance, so they try to saddle atheists with fake claims of intolerance in hope of getting them to self-censor. Perhaps others will refuse to pay any attention to atheists' criticisms on the assumption that they are just being mean and intolerant.
This is ethically and intellectually deplorable. I hope that no atheists, freethinkers, or skeptics take these people seriously; if anything, such statements should be seen as a sign that atheistic critiques of religion are starting to afflict the comfortable and discomfit those who had grown used to their positions of intellectual respectability. In other words, it's a sign that atheistic critiques of religion are having an impact and that's a reason to keep pressing forward.