I think A Case for the Existence of God far and away deserved the Pulitzer Prize this year, over and above all three that the jury listed.
That said, once I saw who was on the jury this year, I am not surprised it wasn't even short-listed. It's very clear to me that a play by Sam Hunter really stood little to no chance with that particular jury. I'm not sure I would call this a rational argument for their choice, but I'm not at all surprised.