Commentaries:
Here as elsewhere, the cloud hides God so people do not succumb, overcome by the brightness of His glory. But the same cloud also provides the opportunity for the Father to reveal a truth He deemed exceedingly important to the three disciples present on the occasion, namely, the opportunity to teach them that the words of His Son carried more weight than the words of Moses or the prophets (represented by Elijah). Just as God used His cloud to facilitate the Israelites' hearing of Moses (Exodus 19:9), so on this occasion the cloud facilitates the disciples' hearing of Jesus.
After Christ's resurrection, the apostle John, who was present at the Transfiguration, refers to this incident, connecting it with God's glory: “And the Word became flesh and dwelt among us, and we beheld His glory, the glory as of the only begotten of the Father, full of grace and truth” (John 1:14). Years later, Peter, who was also present with the brothers James and John at the Transfiguration, likewise connected it with the glory of God: “For He received from God the Father honor and glory when such a voice came to Him from the Excellent Glory: 'This is My beloved Son, in whom I am well pleased'” (II Peter 1:17). Generally, God's cloud reflects His glory by virtue of the fact that He is present in it.
Charles Whitaker
Clouds (Part Two): God's Cloud as His Chariot