What does Mark 6:49 mean?

"Ghost" is from the Greek root word phantasma and refers to an apparition or specter. Jewish tradition taught that demons wandered the wilderness and sea, so the Twelve may think Jesus is a demon. Ironically, they are afraid of the One who is actually there to save them! They like the kind of power which gives them notoriety among the people, but, similar to the people of Gennesaret (Mark 5:14–17), they fear power they can't understand (Mark 4:35–41).

Paul talks about the inability to discern spirits in 1 Corinthians 2. God made us with spirits that can get some sense of the spiritual world, but we primarily live in our physical bodies in the physical universe. Like the Pharisees from Jerusalem who claim Jesus' power came from Satan (Mark 3:22), without the guidance of the Holy Spirit, we cannot recognize the difference between God's Spirit and demons. Jesus promises that those who accept Him as Lord and Savior will receive the Holy Spirit so that they can know the truth (John 14:15–17).

The Twelve have followed Jesus for some time by now. They have seen Him calm a raging sea (Mark 4:35–41), show authority over evil spirits (Mark 5:1–13), and raise the dead (Mark 5:35–43). But they do not yet have the Holy Spirit, and they are not softened to His leading. Before we receive the Holy Spirit, His job is to turn our lost, rebellious hearts toward Christ; it is after, as we are sanctified, that our spiritual discernment grows. We shouldn't get too frustrated when non-Christians miss simple spiritual truths. Until they are willing to listen to the Holy Spirit, those truths will not be available to them (1 Corinthians 2:14).