The debate over the meaning, tone, and quoted history of Obama's address at the National Prayer Breakfast keeps on rolling, and there have been several excellent essays recently:
...The vastly different environments of pre–civil rights America and the modern-day Middle East belies the substantive similarities between the fairly recent religious violence of our white supremacist forebears and that of our contemporary enemies. And the present divide between moderate Muslims and their fanatical opponents has an analogue in our past divide between northern Christianity and its southern counterpart.
This isn’t relativism as much as it’s a clear-eyed view of our common vulnerability, of the truth that the seeds of violence and autocracy can sprout anywhere, and of the fact that our present position on the moral high ground isn’t evidence of some intrinsic superiority.
The point (to me) of Obama's most fractious passage was to end the divisive "Us versus Them" mentality of many in the US Christian community against Muslims in general. Taking a look inward, reviewing the grotesque parts of Christian history, can be healthy, useful for building bridges with allies. It's too bad (but not surprising) that hasn't happened.