What does Mark 4:39 mean?The word translated "rebuke" is from the Greek root word epitimao. Literally, it means to assign or acknowledge the value of something. In this case, Jesus judges that the wind is not wanted. It's the same word used when Jesus confronts demons (Mark 1:25; 3:12; 9:25).
"Peace" is from the Greek root word siopao which literally means to be quiet or to refrain from speaking. "Still" comes from the Greek root word phimoo which is to keep quiet as with a muzzle, keep under control, or silence. It's interesting that Jesus addresses elements of the weather like we would a living creature. While God gave humans authority over animals and plants (Genesis 1:28), Jesus created everything on earth and, therefore, has dominion over all creation (Colossians 1:16).
In the Old Testament, we see that only God can control the weather (Psalm 65:7; 89:9; 107:23–32), although those who make their living from the sea can usually predict it (Matthew 16:3). Some Old Testament prophets announce when God would bring or take away rain, or pray for rain based on God's instructions, but they never command weather directly and by their own authority. The disciples have seen Jesus' authority over injuries and illnesses, as well as demons, but they are only beginning to understand who Jesus really is (Mark 4:41). Jesus calms the storm because the disciples are afraid of dying. They need to see that His authority extends to the external circumstances they will meet.
That does not mean that He will deliver them from all harm; this is one of the great ironies in the Christian life. God can control everything and make all things right and we must have faith in Him and be content even when He doesn't act (Philippians 4:12–13).
In Acts 27:13–38, Paul and his entourage get caught in a horrible storm that tears apart their ship and forces them to swim to safety. But because of his faith, Paul is able to use the circumstances to earn the trust of the crew and minister to the people they meet on the island (Acts 28:7–10). Our own spiritual stability is more important than God's exhibition of power over our troubles.