But the LORD hurled a great wind upon the sea, so that there was a great storm on the sea; the ship looked like it might be broken to pieces. Jonah 1:4
Jonah had a clear assignment from the Lord and he instead did the opposite. God's "Plan A" seemed too hard. Jonah didn't know that it was a "Plan A" and that "Plan B" would be harder. When we disobey because we believe that obedience is too hard, we actually send ourselves into "the school of hard knocks." It is ironic that the low road ends up being more painful than the steep path we avoided.
When we have not died to ourselves (Matthew 16:24), we are living for ourselves and we measure things by, "What's in it for me," "How will this make me feel," or "Is this convenient for me?" We evaluate requests from others and from God through our self(ishness).
God had to "bring the bottom up" for Jonah. We might know someone who is going through some hard discipline. We try to rescue them when they have not yet learned their lesson, yielded to God, died to self, or hit bottom. Then God will have to send another, perhaps bigger storm into that person's life in order to bring them to obedience.
In this story, God sent the storm; but every storm is not sent by God. When Jesus calmed the storm (Mark 4:37-39), it was not a storm that God had sent. By the same token, every earthquake and storm is not sent by God to discipline humanity.
Lastly, I believe that we can infer from Jonah, that in his story, God sent the storm because of his disobedience. God loves the whole world and desires that all humanity be saved. But it is God's children who God disciplines, also out of love. What we have here is a calamity coming upon a group of people because of the one person, of whom the story is about. This one person has a problem in his relationship with God that God is dealing with. The storm affects everyone around the one person that God is disciplining.
I think that Christians often think that storms are hitting them or their area because of the "sinners," when it is really God trying to get the attention of the believers. Remember 2 Chronicles 7:14, "If my people who belong to me will humbly pray, seek my face, and turn from their wicked ways, then I will hear from heaven, forgive their sin, and heal their land."