What does John 6:16 mean?

Jesus sends His disciples away from the crowd for several reasons. The crowd is apparently willing to use violence to accomplish their goals (John 6:15). Involving the disciples in political unrest would put them in the crosshairs of the Roman Empire (John 11:48). More than anything else, however, Jesus probably doesn't want them to let the crowd's adoration feed their egos (Matthew 20:20–28; Luke 22:24). All of Christ's miracles are attached to a spiritual lesson, and this one will be no different. Removing His disciples from the situation solves all three of these problems at the same time (Matthew 14:22).

Jesus' feeding of more than five thousand people (John 6:9-14) is the only miracle recorded in all four Gospels. That provides additional context for the incident described here in the gospel of John. The disciples are sailing to the other side of the Sea of Galilee specifically according to the instructions of Jesus (Mark 6:45). They are not disobeying Him, nor are they making an unwise assumption about His will. Jesus told them to get into a boat and head across the water. This is an important lesson about the nature of trials and hardships: not all suffering is the result of disobedience. In fact, sometimes obedience leads us directly into a storm.

Likewise, according to the gospel of Mark, Christ is watching them during their struggle (Mark 6:45–48). John writes his entire gospel under the assumption that the reader is familiar with the accounts of Matthew, Mark, and Luke. This is why the next verse (John 6:17) will simply state that Jesus "had not yet come" out on the water. Even while the men were afraid, and agonizing over their situation, they were under His watchful eyes.