Because there is still a big problem here. The problem is Jonah. God had more trouble with his backsliding prophet than he had with a whole city full of pagan sinners. Not just a little bit upset. Mad enough to die.
Anger is a great diagnostic tool.
It's eruption is the signal that something is wrong. When you see anger you are onto something very important. Jonah is boiling because the whole city turned to God. Jonah was a bit overwhelmed by God's Grace. Jonah had left holy ground.