Because the Lord disciplines those he loves, as a father the son he delights in. —Proverbs 3:12
St. Augustine said that God loves every person as though there were no one else to love. Likewise, He deals with each of us as though there were no one else to deal with. He knows all about us and therefore knows what it takes to get our attention. The way God gets our attention and brings us to a degree of humility is by manifesting His glory.
But are you ready for this: the thorn in the flesh is actually a manifestation of God's glory. If you pray for God to manifest Himself to you, you might say, "A thorn in the flesh is not exactly what I had in mind!" But there are many ways God shows up, both corporately and individually. Giving us a thorn is not the only way God manifests His glory, I am happy to say, but certainly this was one way in which He communicated with Paul and to each of us. See your own thorn as God's weighty stature in your life, the dignity of His will for you at this time.
As well as being a manifestation of God's glory, the thorn in the flesh is a severe form of chastening or disciplining. I will never forget my first introduction to the idea of being chastened. In that moment I felt an impulse to turn to Hebrews 12:6, which said, "For whom the Lord loveth he chasteneth, and scourgeth every son whom he receiveth" (KJV).
This verse gave me some comfort, but the pain did not go away. It was my introduction—not to the thorn in the flesh—but to the subject of chastening. I knew God Himself was behind everything that was happening. I could live with that. Can you? Just to know that the whole thing is of God.
The thorn in the flesh, then, is from God, and it is a way of making us learn. Nothing else will work for us at the time. So God, who knows this, sends the thorn. It is not unlike what C. S. Lewis calls "severe mercy."
Excerpted from The Thorn in the Flesh (Charisma House, 2004).