At Atheist Persepective, in a post, Moderate Christians - Take some responsibility, stop blaming Dawkins contained this statement:
Many atheists are intolerant of religion. Why? I won’t speak for Dawkins but my own intolerance is triggered by the dishonest and reprehensible conduct of those who purport to spread the love of Christ’s teachings, when, in actual fact, they cause fractions in society and hinder our ability to move forward as a species because of the absolutes they feel so comfortable wallowing in.
If one's object of disapproval is those who 'cause frictions in society and hinder our ability to move forward as a species', then it would seem that these should be the objects of one's intolerance, not 'religion', unless one can argue that the two are identical.
Unless one can prove an identity between the two groups, then the argument is just as valid as saying that one's intolerance of blacks is supportd by the 'reprehensible conduct of those who join gangs and engage in the drug trade'. Such an attitude is blaming the guilty with the innocent, which is entirely unjust.
I have no intolerance for religion. Instead, I have an intolerance for those who advocate policies that promote death, disease, injury, injustice, and ignorance. I am intolerant of these people even when I discover that they are atheists - because it is not religion that I dislike, but the harms inflicted on others. Turning this dislike into a dislike of religion has two bad side effects. First, it condemns those who are innocent because the innocent happen to be religious (even if it is a religion tht says to trust others). Second, it lets the guilty off the hook where the guilty happen not to be religious.
When casting blame (and praise) about, there is a particularly high level importance to coloring inside the lines - blaming those who are actually guilty, and refusing to punish or condemn those who cannot be proved to have contributed to the harm done.