They that were in the ship. I understand these words to refer not only to the disciples, but to the sailors and other passengers. So then those who had not yet declared that he was their Master, instantly acknowledge that he is the Son of God, and by this term render to him the honor of the Messiah. Though at that time this lofty mystery was not generally known, how God was to be manifested in the flesh, (1-Timothy 3:16,) yet as they had learned from the prophets, that he who was to be the Redeemer would be called the Son of God, those who under this designation proclaim the glory of Christ, declare their belief that he is the Christ. [1]

Footnotes

1 - "Declarent qu'ils croyent qu'il est le Christ et le Messins;" -- "declare that they believe that he is the Christ and the Messiah."

Thou art the Son of God - It is probable that these words were spoken either by the sailors or passengers, and not by the disciples. Critics have remarked that, when this phrase is used to denominate the Messiah, both the articles are used, ἑ υιος του Θεου, and that the words without the articles mean, in the common Jewish phrase, a Divine person. It would have been a strange thing indeed, if the disciples, after all the miracles they had seen Jesus work - after their having left all to follow him, etc., were only now persuaded that he was the promised Messiah. That they had not as yet clear conceptions concerning his kingdom, is evident enough; but that they had any doubts concerning his being the promised Messiah is far from being clear.

Then they that were in the ship,.... Not only the rest of the disciples, who remained in it, whilst Peter came forth out of it, to walk upon the sea, to go to Christ: but the mariners also, the owners of the vessel, and their servants that managed it,
came and worshipped him: not merely in a civil, but in a religious way; being convinced, by what they saw, that he must be truly and properly God, and worthy of adoration;
saying, of a truth, thou art the Son of God: not by creation, as angels and men, nor by office, as magistrates, but by nature; being of the same essence, perfections, and power, with God, his Father: and which these actions of his now done, as well as many others, are full attestations of; as his walking upon the sea, causing Peter to do so too, saving him when sinking, and stilling the wind and waves upon his entrance into the vessel; all which being observed by the disciples and mariners, drew out this confession upon full conviction from them, that he was a divine person, and the proper object of worship.

They that were in the ship came and worshipped him. Not only did they approach him with an outward unforbidden gesture of worship, "but they avowed him, for the first time collectively, to be the Son of God."

Thou art the Son of God - They mean, the Messiah.