The author does say:

Only a fool would build a bridge between himself and the people who are actively trying to hurt him. Well, a fool or else a masochist. My default impulse is to play ambassador and take the diplomatic approach. I always try to be accommodating and conciliatory, but there are circumstances under which “building bridges” is a bad idea because certain people will only use that opportunity to hurt others.

Civil discourse is not always appropriate or possible. One must use their best judgment in each circumstance. I thought the article provided a helpful guide should having a mutually respectful conversation with someone who doesn't agree with you be your goal. The author lives in the bible belt in the US, which is not an atheist friendly environment from what I understand. He is a highly visible and vocal athiest in a trying circumstance, and I think it's admirable that he is so patient and level headed. I'm not really sure what the alternative is as I don't know a place on earth where there is no history of animosity between groups and everyone gets along perfectly. It's also worth noting that the author is a former evangelical Christian, so I'm sure that informs his opinion on this as well. I don't think he would be calling for civil discourse in a circumstance where there was any possibility of being so persecuted as the quote describes.