Here we have the problem that reasonable arguments and the self-evident truth of rationality is often only clear among people who already agree on everything of substance. People who agree can confidently assert the rationality and reasonableness of their arguments to those who have the exactly same perspective. So, for example, you have educated people like William F. Buckley, Jr. explaining that there is more evidence of the resurrection of Jesus Christ than that Abraham Lincoln gave the Emancipation Proclamation.

The correct explanation of the described phenomenon is that people often have different ideas about what is reasonable. Khan's interpretation "reason is suspect" appears either as if he doesn't want to prefer his own definition of reason over, say, a religious fundamentalist definition, or as if he practically identifies reason with "everything people call such". Which doesn't seem reasonable according to my definition of reason.