The scene is not a good one. John is in prison for doing good. It doesn't look good for him. He is rough and tumble, and says it like it is. Now he is saying I doubt. It may only be a little, but he is having a crisis of faith of sorts. Hard times have come and things aren't working out like he thought. So, in the place of torment he asks, "Are you really the Messiah?" John saw heaven open, heard God speak, saw the Spirit descend on Jesus among many other things. He experienced God in the miraculous. Hard times have a way of erasing our memory don't they? Now, because of what he is going through, he is having second thoughts or at least needs to have some confirmation that he is correct and his hard times aren't for not.
So how does Jesus respond to his cousin's second thoughts and doubts? He backs him up! Instead of a "yes, it's me," Jesus points to his life which is pretty incredible. Then he out and out promotes John! John was doubting and Jesus starts promoting! This is so fantastic. Do you get it? Jesus' heart was not to hold John accountable, or to reprove him for weakness, it was to promote him.
He hasn't changed. When we are weak, when we doubt, when we struggle, Jesus promotes us. He brags on us. He calls us great. Incredible! Is that your Jesus? Is that your Father in heaven? Jesus said if you see Him it is like seeing the Father. Is that your Father? If not, then change your mind and get free.