What does Matthew 17:6 mean?

The response of the disciples is familiar and reasonable. Overshadowed by the presence of God the Father, seeing figures like Moses and Elijah, and spoken to by the voice of God the Father, they are terrified. They fall on their faces, which is both a common expression of both terror and one of reverence. This is an entirely natural and completely appropriate response to any encounter with God.

Prior to this, Peter seems to have understood on an intellectual level that Jesus was the Son of the living God. He had said so in response to Jesus' earlier question (Matthew 16:13–16). Twice since then, however, Peter had shown that he did not yet fully understand that being the Son of the living God meant that Jesus was God. Otherwise, Peter would not have rebuked Jesus when Jesus said that He must suffer and die before being raised on the third day (Matthew 16:21–23). Peter would certainly not have suggested worshipping Jesus alongside Moses and Elijah on the mountain (Matthew 17:1–5).

Peter will eventually come to understand that his natural response to God the Father, falling on his face in fear, is also an appropriate response to God the Son, Jesus. This is the same man who had declared a week earlier that He would come in judgment with His angels and the glory of the Father when He returns to earth (Matthew 16:27).