The recognition of Jesus as the Son of God came gradually. By the time Jesus asked the disciples who they said He was, Peter knew He was the Christ. Knowing something with your head is one thing. Knowing it with your heart, knowing it with every fiber of your being, is a little different. That knowing came gradually, and this experience on the mountain was a significant part of their understanding.
When the cloud overshadowed them and the disciples began to enter the cloud, they knew this was no ordinary cloud, and they were afraid. Thayer describes their reaction to the cloud as being "seized by alarm" as one "startled by a strange sight or occurance". It would be odd if they hadn't been frightened. What came next, though, must have been even more frightening. They heard the Voice of God speak audibly, instructing them to listen to Jesus and affirming Jesus as God's Son and Chosen One. That voice left no doubt about Jesus and His identity.
You might think that the cloud and the voice would be such a memorable experience for them that these men would never fail Jesus again. Even after this dramatic experience, however, Peter, James, and John would struggle with faithfulness. Having heard that voice and seen those sights, Peter would still deny Him and the rest of the disciples would run away when He was arrested. Years later, those three men would be willing to lay down their lives for Jesus. John would be exiled to Patmos. Peter and James would die martyr's deaths. That willingness to put everything behind them and follow Jesus without reservation did not come all at once. It did not come with any great burst of insight. It did not come when they were overcome by the cloud and heard God's voice. Total surrender came a little at a time, relinquishing one bit of control after another, until obedience to Christ was all that mattered. Their personalities were much the same, but their flaws were changed, their rough edges smoothed.
Our tendency is to see Peter in terms of his denial of Christ, to remember the disciples in terms of their desertion of Jesus in His most difficult hours. It is our tendency to see others in terms of their failures, but Our Lord gave incredible grace and mercy to His followers. From all their failure, He brought growth and maturity, and, ultimately, victory. He could be patient with the process because He knew the end result. He did not plan to leave them as they were, nor does He plan to leave us the way He found us.
Just as He is patient with us as our faith and our understanding of who He is grows and matures, we, too, must be patient with those who are not as far along on their journey. It will not likely be in a flash of insight that maturity comes, but, over time, God will give the increase to the seeds that are sown along the way. Growth can come, even for those who seem most unlikely to mature as disciples.
Be patient. Extend grace. Treat others with the mercy Christ Himself has extended to you. The end of our earthly maturing hasn't come until that last breathe is drawn and we step into eternity, so keep hoping, keep sowing seeds, and most of all, keep praying.