(ubi sup.) Or else the ship into which He embarked, is taken to mean the tree of His passion, by which the faithful attain to the security of the safe shore. The other ships which are said to have been with the Lord, signify those, who are imbued with faith in the cross of Christ, and are not beaten about by the whirlwind of tribulation; or who, after the storms of temptation, are enjoying the serenity of peace. And whilst His disciples are sailing on, Christ is asleep, because the time of our Lord's Passion came on His faithful ones, when they were meditating on the rest of His future reign. Wherefore it is related, that it took place late, that not only the sleep of our Lord, but the hour itself of departing light, might signify the setting of the true Sun. Again, when He ascended the cross, of which the stern of the ship was a type, His blaspheming persecutors rose like the waves against Him, driven on by the storms of the devils, by which, however, His own patience is not disturbed, but His foolish disciples are struck with amazement. The disciples awake the Lord, because they sought, with most earnest wishes, the resurrection of Him whom they had seen die. Rising up, He threatened the wind, because when He had triumphed in His resurrection, He prostrated the pride of the devil. He ordered the sea to be still, that is, in rising again, He cast down the rage of the Jews. The disciples are blamed, because after His resurrection, He chid them for their unbelief. And we also when being marked with the sign of the Lord's cross, we determine to quit the world, embark in the ship with Christ; we attempt to cross the sea; but, He goes to sleep, as we are sailing amidst the roaring of the waters, when amidst the strivings of our virtues, or amidst the attacks of evil spirits, of wicked men, or of our own thoughts, the flame of our love grows cold. Amongst storms of this sort, let us diligently strive to awake Him; He will soon restrain the tempest, pour down peace upon us, give us the harbour of salvation.
Source: Catena Aurea by Aquinas