The first time the Bible uses a word or concept frequently sets the stage for how God inspired the human writers to use it throughout the rest of His Word, and clouds are no exception. We find clouds first described immediately after the Flood, where they are linked to the sign of the rainbow and God's everlasting promise that He will never again flood the earth.
Today, we are far removed from the events of the Flood, so it may be difficult to grasp what it and its aftermath were like—every man, woman, and child dead, except Noah and his family. From the genealogies, we know that humanity had been on the earth about a millennia and a half, and before the Flood, people lived much longer lives and produced numerous children. Only God, and perhaps the angelic host, knows how many millions or billions of people that cataclysm destroyed.
God forcefully and deliberately ended that age. Yet, lest we think that all is hopeless and that another worldwide catastrophe could wipe out all life on the planet, God gives us this promise, repeating it several times: He will not destroy all flesh again.
Of course, we know from many verses that the destruction at the end of this age will involve fire rather than another worldwide flood. But this does not nullify God's promise. The point remains that God will not destroy all flesh by any means, whether by flood or by fire.
Genesis 9:12-17 indicates that the rainbow is the sign of that promise, but they also show that the setting and the context of that promise is the clouds. In the promise we see elements of God's faithfulness, but the backdrop is God's mercy in not destroying all of mankind.
An interesting parallel to this appears in the book of Revelation. Genesis and Revelation mirror each other in many ways; frequently, when a matter is introduced in Genesis, it is resolved or concluded in some way in Revelation. As bookends of the Bible, they contain many of the same themes. Notice what John describes in Revelation 10:1:
I saw still another mighty angel coming down from heaven, clothed with a cloud. And a rainbow was on [H]is head, [H]is face was like the sun, and [H]is feet like pillars of fire.
Studying into this chapter makes plain that this Being is no mere angel, but it is in fact Jesus Christ. In the sequence of events, this chapter might be called “the beginning of the end” because it shows the mystery of God being finished and the point at which there would be no more delay in everything reaching its conclusion.
Here at the end, John's vision pictures Jesus with a rainbow, showing that He has not forgotten His promise to mankind. Even as He is about to unleash tremendous destruction on rebellious humanity, the sign of His promise not to destroy everyone is literally at the top of His head. Notice that He is also clothed with a cloud. It is covering Him, allowing only the brightness of His face and the fiery brilliance of His feet to show.
To understand the significance of this cloud, consider what a cloud is and does. By way of definition, a cloud is “a visible mass of droplets of water or frozen crystals, suspended in the atmosphere.” Sometimes clouds bring rain, which can be either a blessing or a curse depending on the circumstances, but other times they pass by without sharing a drop. Nevertheless, there is one thing a cloud will always do, if it has any size at all: It will impede light, such as the light of the sun or the moon. Since it is clothing Jesus Christ, this cloud filters some of His breathtaking glorious radiance. This covering is critical because the undimmed brightness of a God-being is lethal to mankind. Jesus Christ will be returning in glory, and that awesome glory has a terrible, lethal effect on sinful flesh.