The sailors were horrified. Jonah's answer terrified them: "Then were the men exceedingly afraid." They now knew the storm came from the God who made the sea, and that Jonah was running from Him. Their words are less a request for information than a cry of alarm. Keil & Delitzsch say the Hebrew is not a question about the nature of his sin but "an exclamation of horror" at his flight. Gill says they wondered he would act "such a foolish part" as to flee from the God he had just described. Matthew Henry puts their thought this way: "If thou fearest the God that made the sea and the dry land, why wast thou such a fool as to think thou couldst flee from his presence?"

Jonah offers no excuse. The narrator explains instead: "For the men knew that he fled from the presence of the LORD, because he had told them" (Jonah 1:10). The sailors' next question is practical, "What shall we do unto thee, that the sea may be calm unto us?" (Jonah 1:11), and Jonah answers by owning the blame: "for I know that for my sake this great tempest is upon you" (Jonah 1:12).

In Hebrew the sailors' words are mah-zoth asita, literally "What is this you have done?" That is why the ESV prints it as an exclamation: "What is this that you have done!" The Hebrew verb behind "he fled" describes a flight still underway: Jonah "was fleeing." The sailors knew this because, as Gill notes, "Jonah told the whole story at length, though the whole is not recorded." On Jonah 1:3, Keil & Delitzsch explain that fleeing "from the presence of the LORD" meant leaving the land where the LORD dwelt in the temple and withdrawing from His service. Jonah was stepping away from serving God.

The question exposes the gap between what Jonah said and what he did. He said, "I fear the LORD" (Jonah 1:9), yet it is the heathen sailors (men who did not know the LORD) who tremble. Their fear grows through the chapter: they "were afraid" of the storm (Jonah 1:5), "exceedingly afraid" at Jonah's words (Jonah 1:10), and at the end they "feared the LORD exceedingly, and offered a sacrifice unto the LORD, and made vows" (Jonah 1:16). God uses even His prophet's disobedience to bring these men to fear Him.

Later Jonah gives his own answer to "Why?": "Therefore I fled before unto Tarshish: for I knew that thou art a gracious God, and merciful" (Jonah 4:2). He did not run because he doubted God's power. He ran because he knew God's mercy.