Looking at this Matthew Henry quote, it's a common mistake for just anyone including a Christian to think that extraordinary afflictions are always punishments. It is very easy to think about it that it's easy to get envious of the prosperity of the wicked while good men experience chastisement.
David said in Psalm 73:3-9 that he was envious at the prosperity of the wicked. Whenever I look at the news, I tend to feel that life's unfair and I want to ask God why He allows wicked men to prosper while the redeemed of God are allowed to suffer. A picture of that happens during the Dark Ages when the corrupt Papal courts flourished, they had a beautiful basilica in Vatican City while the true saints of God are afflicted to no end. Reading through the Foxe's Book of Martyrs, I always wanted to question why God allowed such things to happen then I read my Bible for the answers.
What many fail to see is that God has a purpose for affliction. As Thomas Watson said, "Afflictions add to the saint's glory. The more the diamond is cut, the more it sparkles; the heavier the saints' cross, the heavier will be their crown." 1 Peter 1:7 says that the trial of one's faith is more precious than gold. James 1:2-4 says that the trial of one's faith must be counted with all joy towards perfection. When a Christian is allowed to suffer, there is a purpose. Looking at Job's sufferings, he said in Job 13:5 that he will trust in God even if it means his life is at stake.
A Christian cannot be more effective unless God removes the dross. 1 John 2:8 says that if we say we have no sin, the truth is not in us. Hebrews 12:5-7 says that God chastises those He loves. Sometimes, God's allowance of extraordinary afflictions are meant to keep the Christian in the path of purity. 2 Corinthians 12:10 says that Paul actually takes pleasures in the trials of the Christian life because God has a special purpose for them. It does sound stupid with the natural man but the Christian slowly understands the purpose of pain and suffering is in shaping up the Christian life.