At issue is a discussion about the violence committed by the church in the past, and how atheist use that against Christianity while excusing away the atrocities of known atheist regimes. This is a fairly common tactic employed by atheist apologists. I’ve heard several atheists try to use the historical fact of the church’s sometime horrible activity to invalidate religion wholesale. McKnight will point out the obvious inconsistencies in their argumentation.
McKnight’s summary of the book being discussed is good, but I found the discussion thread particularly interesting. Take the time to read through the comments.