I wouldn't have him ask questions. Your father is an authority figure and your son will feel strong pressure to accept whatever BS answer is given him. Better to explain that some people just believe very silly things (and maybe give examples of things from other religions that everyone will agree are silly). Then nurture his intellect and critical thinking skills and it won't be long before he has no interest in bible study.
Take that for what it's worth, coming from someone without kids. I do, however, strongly believe that had someone, anyone, done that for me, I would never have been baptized.