In Matthew 3:13-17, John the Baptist meets Jesus and is resistant to baptizing him because he "seemed" to know that he was the Messiah and he thought that Jesus should baptize him instead. Did John see the clouds open up and hear God's voice? Later, in Matthew 11:2-6, when he was in prison he sent two of his disciples to ask Jesus was he the one. Why was he doubting if he saw the clouds open up and heard God's voice?
Yes, John did see. "And John bore witness, saying, 'I saw the Spirit descending from heaven like a dove, and He remained upon Him. I did not know Him, but He who sent me to baptize with water said to me, 'Upon whom you see the Spirit descending, and remaining on Him, this is He who baptizes with the Holy Spirit.' And I have seen and testified that this is the Son of God'" (John 1:32-34).
John’s Doubts (Matthew 11:2-6; Luke 7:18-23)
Eventually news of Jesus’ raising of the widow’s son reached the ears of John, who was in prison. John sent his disciples to Jesus to ask, “Are you the Coming One, or do we look for another?”
It seems to be a strange question coming from the man who prepared the way for Christ and declared him to be the Messiah at his baptism. Yet, we must remember that John was a man, like all the other prophets before him. Other prophets had their moments of doubt. Moses had to be convinced to go and free the Israelites (Exodus 4:1-17). Gideon asked for two miracles before he lead God’s people to war (Judges 6:36-40). Elijah gave up after Jezebel threatened his life (I Kings 19:1-10). Jeremiah cursed the day he was born (Jeremiah 20:14-18). Remember that John has been in prison for quite a while now. Perhaps he thought, as did so many Jews, that Jesus would lead Israel in triumph against the Romans. Yet in all this time, Jesus hasn’t declared himself, nor has there been any apparent move to re-establish the kingdom of Israel. And for John, there has been no rescue. Is it a wonder that John began to doubt himself?
Jesus didn’t answer John’s disciples directly. Instead during that very hour that they asked, he performed numerous miracles before the disciples of John. Afterwards he told them to return to John and tell them what they witnessed. His reply back to John echoes the words of Isaiah 35:5-6 and Isaiah 61:1, but the hidden message is found in the verse before. “Say to those who are fearful-hearted, "Be strong, do not fear! Behold, your God will come with vengeance, with the recompense of God; He will come and save you"” (Isaiah 35:4). Jesus was telling John to take courage. Jesus warns John not to fall away because Jesus was not meeting John’s personal expectations.