John Chrysostom

"When the disciples," it is said, "saw Him walking on the sea, they were troubled, saying, It is a spirit: and they cried out for fear." Yea, and He constantly doth so; when He is on the point of removing our terrors, He brings upon us other worse things, and more alarming: which we see took place then also. For together with the storm, the sight too troubled them, no less than the storm. …

Homily on the Gospel of Matthew 50 ↗

Theophylact of Ohrid

But they thought it was a phantom, so extraordinary and strange was the sight. For they did not recognize Him by figure, because it was night and because of fear.

Commentary on Matthew ↗

Augustine of Hippo

But in the fourth watch of the night, which is the end of the night—for one watch consists of three hours—the Lord comes to aid at the end of the age, and He is seen walking on the waters. Although this ship is troubled by the storms of temptation, it nevertheless sees God glorified walking over all the swells of the sea; that is, over all the principalities of this world. …

Sermon 75 ↗

Jerome

And when the disciples saw him walking on the sea, they were troubled, saying: It is a ghost. If, according to Marcion and Manichaeus, our Lord was not born of a Virgin, but appeared in a vision: how is it that now the apostles fear seeing a vision? And they cried out due to fear. The confused shout and uncertain voice is a sign of great fear.

Commentary on Matthew ↗

Thomas Aquinas

And seeing him. Here the effect of Christ's presence is presented, namely the disturbance of the disciples; hence the disturbance is presented, the cause is presented, and the sign. And he says and seeing him, they were troubled etc. You should know that when divine help is most near, the Lord allows a greater affliction, so that then his help may be received with greater devotion and thanksgiving. Likewise, fear increased all the more, because frequently men are converted through fear. And why? …

Commentary on Matthew ↗