He was relating his story to you, that he was every bit a committed Christian that you think you are, and then he began to investigate, and ultimately realized, there were no good reasons to believe any longer. What you fail to see is, this says more about your insecurities in your personal faith than it does about him. It scares you to even consider the fact that if a "true" Christian, like me, or Kvothe, used to be, could lose our faith, your only option is to double down, and deny anyone else their personal experience. In your arrogance, you have basically accused Kvothe of not being a "true" Christian and not really knowing god existed. This is why he stated that maybe you were "talking past each other."