When Jesus encounters doubt in his disciples he asks why, so that the doubter can explore where their doubt is coming from, and return their focus to Jesus and the relationship they have with him.
From Winn Collier.
When Jesus encountered doubters, he did not leave them to wallow in their uncertainty, but neither did he rail against their human frailty. Jesus showed his pierced hands to Thomas. Jesus met Nicodemus in the middle of the night. Jesus healed the demon-possessed son of the father who pleaded, “I do believe; help me overcome my unbelief!” And here, with Peter, Jesus did not leave him to drown, nor did he heap vitriol on his wavering faith. Rather, Jesus pulled Peter from the water and asked him a question. Why?
Doubt as a barrier to trust is where Jesus takes aim. Jesus doesn’t mind questionsHe gives time and space for people to hear and consider and journey into the truth. Peter’s doubt, in fact, had nothing to do with philosophical quandaries or historical veracity. Peter did not have a theological dilemma. Peter did not slip into the waves because of an existential crisis. Peter wavered in trusting his friend. His issue was not creedal, it was relational.
Whatever pushed Peter to doubt, it was obviously connected to fear, understandably so. The disciples had been on pins and needles the entire night. IN a quick turn of events, Peter found himself alone on top of the waves out in the middle of a blustery storm. This doubt had nothing to do with logic or reason. There was no process that led Peter here. An apologetics lecture or a philosophical conversation would not have helped. Often we believe our doubt would be assuaged if God would miraculously intervene in the world. No miracles would have aided Peter. He had just lived the miracle, a few extraordinary aquatic steps. Peter’s doubt detonated in a flash, because all of a sudden he thought he might drown – and his fear was larger than his trust in Jesus..
Winn Collier, Holy Curiosity, Baker Books, 2008, pgs 136, 137-138.