Various reasons for prophet Jonah’s disobedience to Yahweh have been suggested. Often when the story is introduced an emphasis is placed on the violent nature of the Ninevites (Nahum 3:1 calls it the “bloody city”.) No doubt thoughts of danger entered the prophet’s mind, but this was not the primary reason for Jonah’s unwillingness. Jonah was not motivated to disobedience by the character of Nineveh, but by the character of God.
Jonah 4:2 actually indicates that Jonah had confidence in his wellbeing (because he believed that his preaching would be received). In this verse we find the clearest insight into why Jonah did not want to preach to the Ninevites. “And he prayed to the Lord and said, “O Lord, is not this what I said when I was yet in my country? That is why I made haste to flee to Tarshish; for I knew that you are a gracious God and merciful, slow to anger and abounding in steadfast love, and relenting from disaster” (Jonah 4:2 emphasis added). It was precisely because Jonah knew that God would relent from judgment (implicitly revealing that he knew Nineveh would repent) that he disobeyed. A number of things may be happening here.
Firstly, Jonah likely had a prejudice against the Ninevites (and Gentiles in general), arising from his strong national pride. When the sailors asked Jonah, “What is your occupation? And where do you come from? What is your country? And of what people are you?” (1:8), he apparently skips the first three questions and proudly answers the last. In addition, ironically, he states that he fears (honors, respects, worships) Yahweh who he is presently fleeing (1:9), followed by an elaborate description of this God. It would seem that this supposed ‘fear of Yahweh’ was a statement of national pride rather than a revelation of Jonah’s heart. Jonah was a Hebrew and he was proud of it. Letting personal prejudice get in the way of God’s call is as big of a problem for Christians today as it was for Jonah.
Secondly, Jonah’s desire for Nineveh’s destruction may have been rooted in his desire for Israel’s preservation. Not only could Nineveh’s repentance multiply and accentuate Israel’s guilt (one of its key contributions to the Book of The Twelve), but the ruin of Nineveh would equal one less world-power that could be used in Judgment against rebellious Israel. This hypothesis is discussed (and probably over-emphasized) in Baxter’s Explore The Book. We must not play God as Jonah did, thinking that saving Israel was a noble task, and one worth disobeying God, and even dying, over. Instead we should trust God’s sovereign will, knowing that all things work together for good.
Running completely contrary to emphasis of the Patch The Pirate children’s song “Jonah” which states that Jonah, “did not obey God immediately” and thus he was thrown, “down in the depths of the deep blue sea,” the book of Jonah actually emphasizes God’s mercy and grace. It was Jonah’s desire to be thrown into the sea (1:12), but God chose to show him unmerited favor by saving him from drowning (1:17). God did not need to save Jonah; he could have used anyone to preach repentance to Nineveh, but God had a work of repentance to do in Jonah as well. God does not let us get away with disobedience, but in his grace he pursues us in an effort to save us from our destructive paths.
We see clearly that our God is, “a gracious God and merciful, slow to anger and abounding in steadfast love, and relenting from disaster” (4:2). This grace is not only extended to his chosen people (God saves Jonah from drowning, and later prepares a tree for shade), but also to the Gentile nations (God relents from the disaster he had planned for Nineveh). Some believe that Jonah himself may have written the book of Jonah, which would, of course, imply that he learned his lesson in the end. God is not prejudiced, but wants his Message spread to every nation and people group. The book ends with a question from God (“Should not I pity Nineveh?…”), forcing the reader to either side with Jonah or Yahweh.
 J. Sidlow Baxter, Baxter’s Explore the Book (Zondervan, 1987), 159.
 Ron Hamilton, Jonah, Sing Along with Patch the Pirate, n.d., http://www.majestymusic.com/p-23-sing-along-with-patch-the-pirate-cd.aspx.
 Tullian Tchividjian, Surprised by Grace: God’s Relentless Pursuit of Rebels (Crossway Books, 2010), 169.