They weren’t getting it. You would think that they would have begun to understand that Jesus could and would perform miracles – he had just that morning fed five thousand people with five loaves of bread and two fish.
And who could do that but God alone. Yet, they didn't make the connection that Jesus was God.
The text says that Jesus was walking as if he was going to pass by them. This is a hint to us of Jesus' Deity. He wanted to pass by them, just like God passed by Moses in Exodus 33-34. Jesus wants His disciples to understand that He is God.
They do see Him, but they are terrified.
Jesus shows His great compassion when he says to them, "Take heart. It is I."
Yet, the disciples still don't get it. They are told to take heart, because Jesus, God Himself is with him. Yet they are hard-hearted, and can't see that God Himself, in the person of Jesus, is with them.
They still don't understand.
Perhaps the great challenge for us is to soften our hearts before Jesus, and not let fear keep us from having faith in Him. And perhaps the great comfort is that though His disciples don't really get Him, he still gets in the boat and is present with them.
Today, "take heart. It is I."