Why are you troubled? By these words they are exhorted to lay aside terror, and regain the possession of their minds, that, having returned to the rigor of their senses, they may judge of a matter which is fully ascertained; for so long as men are seized with perturbation, they are blind amidst the clearest light. In order, therefore, that the disciples may obtain undoubted information, they are enjoined to weigh the matter with calmness and composure. And why do thoughts arise in your hearts? In this second clause, Christ reproves another fault, which is, that by the variety of their thoughts they throw difficulties in their own way. By saying that thoughts arise, he means that the knowledge of the truth is choked in them in such a manner, that seeing they do not see, (Matthew 13:14;) for they do not restrain their wicked imaginations, but, on the contrary, by giving them free scope, they permit them to gain the superiority. And certainly we find it to be too true, that as, when the sky has been clear in the morning, clouds afterwards arise to darken the clear light of the sun; so when we allow our reasonings to arise with excessive freedom in opposition to the word of God, what formerly appeared clear to us is withdrawn from our eyes. We have a right, indeed, when any appearance of absurdity presents itself, to inquire by weighing the arguments on both sides; and, indeed, so long as matters are doubtful, our minds must inevitably be driven about in every direction: but we must observe sobriety and moderation, lest the flesh exalt itself more highly than it ought, and throw out its thoughts far and wide against heaven.

Why are ye troubled? - Why are you alarmed or frightened?
And why do thoughts - The word "thoughts" here means "doubts" or suspicions. It is used in this sense also in 1-Timothy 2:8. The doubts which they had were whether he was the Christ. He reproves them for doubting this; for,
1. The Scriptures had foretold his death;
2. He had himself repeatedly done it; and,
3. They had now the testimony of Peter that he had seen Jesus alive, and of the angels that he was risen. After all this evidence, Jesus reproves them for doubting whether he was truly the Messiah.

And he said unto them, Why are ye troubled? and why do (g) thoughts arise in your hearts?
(g) Various and doubtful thoughts which fall often into men's heads, when any strange thing occurs, thoughts of which there is no great likelihood.

And he said unto them, why are ye troubled,.... Who had more reason to rejoice, and be glad, as they were when they knew that it was Jesus:
and why do thoughts arise in your hearts? whether what they saw was Jesus, or an apparition, which gave them a great deal of trouble and uneasiness, and filled them with fright and terror; as it was, and is usual with persons when they fancy they see a spirit, or an apparition; see Matthew 14:26.