How do you explain Paul asking three times for the thorn in the flesh to be removed but God's answer was no?
Did Paul not believe enough?
The Work of God to Save- john piper
We know this for two reasons. First, because Paul describes the purpose for the thorn in terms of preventing pride. But Satan's whole design is to produce pride not prevent it. That's how he kills: either with pride in what we have done, or despair over what we haven't done. Paul's revelations in Paradise made him vulnerable to pride and self-exaltation. So God uses the hostile intentions of Satan for Paul's holiness. Satan wanted to make Paul miserable and turn him away from the faith and the ministry and the value of the visions he had seen. But God wanted to make Paul humble and turn him away from self-exaltation. So God appointed the thorn of Satan for the work of salvation.
The other reason we know the thorn is God's work and not just Satan's is that when Paul prays in verse 8 that God would take the thorn away, the Lord says, No, because my power is made perfect in this weakness. In other words, I have a purpose in what is happening to you. This is not ultimately Satan's destroying work. It is ultimately my saving, sanctifying work.
Just like it was with Job—God permits Satan to afflict his righteous servant, and turns the affliction for his good purposes. (See also Luke 22:31–32.)
For What Purpose?
What is the purpose of such weaknesses? Is there a goal or an aim for why the weaknesses come? Why insults, hardships, persecutions, calamities, troubles? Why can't I find a job? Why am I trapped in this awful marriage? Why does my dad have cancer? Why can't I have children? Why do I have no friends? Why is nothing working in my life?
Paul gives three brief answers about his own experience and I think they are tremendously important for us to live by.
Satan's Purpose to Buffet You
First, he says that Satan has the purpose to buffet you or harass you (v. 7). And so it is OK to pray for relief. That's what Paul did until he got word from the Lord. Pain is not a good thing in itself. God does not delight in your suffering. Satan does and he must be resisted.
God's Purpose to Humble You
Second, God's purpose over and through Satan's harassment is our humility. Paul was in danger of pride and self-exaltation and God took steps to keep him humble. This is an utterly strange thing in our self-saturated age. God thinks humility is more important than comfort. Humility is more important than freedom from pain. He will give us a mountain top experience in Paradise, and then bring us through anguish of soul lest we think that we have risen above the need for total reliance on his grace. So his purpose is our humility and lowliness and reliance on him (cf. 1:9; 4:7).
God's Purpose to Glorify Jesus
Finally, God's purpose in our weaknesses is to glorify the grace and power of his Son. This is the main point of verses 9–10. Jesus says, "My grace is sufficient for you, for my power is made perfect in weakness." God's design is to make you a showcase for Jesus' power. But not necessarily the way the market demands: not by getting rid of all our weaknesses; but by giving strength to endure and even rejoice in tribulation.
Let God be God here. If he wills to show the perfection of his Son's power in our weakness instead of by our escape from weakness, then he knows best; trust him. Hebrews 11 is a good guide here. It says that by faith some escaped the edge of the sword (v. 34) and by faith some were killed by the sword (v. 37). By faith some stopped the mouths of lions, and by faith others were sawn asunder. By faith some were mighty in war, and by faith others suffered chains and imprisonment (see also Philippians 4:11–13).
The ultimate purpose of God in our weakness is to glorify the kind of power that moved Christ to the cross and kept him there until the work of love was done. Paul said that Christ crucified was foolishness to the Greeks, a stumbling block to the Jews, but to those who are called it is the power of God and the wisdom of God (1 Corinthians 1:23f.).
The deepest need that you and I have in weakness and adversity is not quick relief, but the well-grounded confidence that what is happening to us is part of the greatest purpose of God in the universe—the glorification of the grace and power of his Son—the grace and power that bore him to the cross and kept him there until the work of love was done. That's what God is building into our lives. That is the meaning of weakness, insults, hardships, persecution, calamity.
It is...