It appears to me that Jesus did not come walking out to save them but had some other lesson in mind?
Mark 6:48
ESV - 48 And he saw that they were making headway painfully, for the wind was against them. And about the fourth watch of the night he came to them, walking on the sea. He meant to pass by them.
For follow-up discussion and general commentary on the topic. Comments are sorted chronologically.
Following is a scenario I have been exploring that may explain why Jesus would plan to pass them by.
Earlier in Mark's gospel Jesus sent his disciples out to minister with his power and authority. They experienced real supernatural power for the first time. They came back overwhelmed by the effects which fueled their pride, arrogance and independence. They said to Jesus, "Even the demons obey us".
Jesus recognized the corruptive influence of this power and wanted to get them away to a quiet place so he could warn them of these affects.
But the people wanted Jesus to teach them and there were thousands of them.
At the end of a long day the disciples tell Jesus he needs to disband the meeting so the people can go find something to eat (they start telling Jesus how to run his ministry). So Jesus says to the disciples "you feed them". Indignant, Jesus confronts their arrogance by challenging them to find the resources without him.
Then he tells them to get into the boat and go across the lake as he would join them later - a strange request. Jesus, sitting on the hillside, then watched them throughout the night.
I believe Jesus created the storm to impede their progress so they would learn how helpless they are relying on their own resources. But they don't pray for help.
Then Jesus starts walking across the lake and intends to walk right by them to show how superior his resources are. When they finally cry out for help, compassionately he joins them and calms the storm.