How could such a prayerful man as Jonah drift away from his calling and fall into disobedience? It begins with a partial, incomplete knowledge of God's nature.
Jonah was given a powerful revelation of God's grace and mercy. He testified, "I knew that thou art a gracious God, and merciful, slow to anger, and of great kindness, and repentest thee of the evil" (Jonah 4:2).
Jonah claimed this revelation was the reason he ran away: "Therefore I fled before unto Tarshish" (4:2). By his actions he was saying, "Lord, You so easily forgive all who repent. Every time you pronounce judgment, You are overcome with mercy. I know You're not going to judge Nineveh. As soon as I prophesy, they'll repent, and You'll pour Your grace on them."
Do you see the problem with Jonah's reasoning? He is describing only a partial revelation of God's nature. And he is accusing God of being soft on sin. Of course, God is everything Jonah describes here: longsuffering, willing to forgive, ready to pour out abundant grace. I thank God for this marvelous revelation of His nature. It has been the most life-giving truth I have ever known. I love preaching mercy to God's people.
But the Bible also speaks of God's holy, righteous nature. "The wrath of God is revealed from heaven against all ungodliness and unrighteousness of men, who hold the truth in unrighteousness" (Roman 1:18). Surely Jonah knew this side of God. How could he neglect it?
I believe Jonah had no understanding of the fear of God. If you think of God only as merciful, you will find it easy to disobey His Word. You'll believe He esteems His warnings lightly, that He doesn't mean what He says. I believe this was the root of Jonah's disobedience.
Such fear has to be sought diligently. And it must be implanted in us by the Holy Spirit: "If thou seekest her as silver, and searchest for her as for hid treasures; then shalt thou understand the fear of the Lord, and find the knowledge of God" (Proverbs 2:4-5). Like God's mercy, the fear of God is life-giving: "The fear of the Lord is a fountain of life, to depart from the snares of death" (Proverbs 14:27).