First of all, it is possible that God has reasons for allowing evil to exist that we simply cannot understand. In this the Christian can have confidence in God knowing that His ways are above our ways (Isaiah 55:8-9). As the Bible says, the just shall live by faith (Hab. 2:4).
Second, God may be letting evil run its course in order to prove that evil is malignant and that suffering, which is the unfortunate product of evil, is further proof that anything contrary to God’s will is bad, harmful, painful, and leads to death.
God gave Adam dominion over the world (Gen. 1:28). When he rebelled against God, he set in motion an entire series of events and changed the very nature of man and creation. Both were affected by sin. Creation was no longer a paradise but bore thorns and thistles (Gen. 3:17-18; Rom. 8:22). People became sinful (Rom. 5:12; Eph. 2:3), who were haters of God (Rom. 3:9-12), etc. The only conclusion to such a situation is death. Jesus said, “And except those days should be shortened, there should no flesh be saved: but for the elect’s sake those days shall be shortened” (Matt. 24:22).
Sin is rebellion against God and His created order, but God has not left us alone in this fallen world. He continued to enter this world–pointing us to Himself, to truth, to morality, purity, and love. He used the evil of the world (liars, perjurers, the envious, etc.,) to bring His Son to the cross so that we might have the opportunity to obtain eternal life. In this, God has not stepped away from fallen creation but has stepped into it by becoming Jesus. God works within the fallen world to effect change, and He uses fallen people to accomplish His will. In this, He is proving His sovereignty over evil, suffering, and rebellious people–proving that sin and evil are utterly futile and that He is worthy of honor and glory.
A third possible reason that God is letting evil occur is so that on the day of judgment, the condemned will have no right to say that their sentence is unjust. God is not stopping people from exercising their free will. Think about this: If someone said that God should stop evil and suffering, then should God then stop all evil and suffering? If God only stopped some of it, then we would still be asking the same question of why it exists.
So, if we want God to stop evil and suffering, then He must stop all of it. We have no problem with this when it means stopping a catastrophe or a murder or a rape. But what about when someone thinks of something evil? Evil is destructive whether it is acted out or not. Hatred and bigotry in someone’s heart is wrong. If it is wrong and if God is to stop all evil, then He must stop that person from thinking his own thoughts. To do that, God must remove his freedom of thought. Furthermore, which person on the earth has not thought something evil? God would be required, then, to stop all people from exercising their free will. This is something God has chosen not to do. Therefore, we could say that one of the reasons that God permits evil and suffering is that of man’s free will.
Fourth, it is quite possible that God uses the suffering to do good. In other words, He produces patience through tribulation (Rom. 5:3). Or He may desire to save someone through it. Take for example, the account of Joseph who was sold into slavery by His brothers. What they did was wrong, and Joseph suffered greatly for it. But, later, God raised up Joseph in Egypt to make provisions for the people of that land during the coming drought of seven years.
Not only was Egypt saved but also his family and brothers who originally sold him into slavery. Joseph finally says to them, “You meant it for evil, but God meant it for good” (Gen. 50:15-21).
Of course, the greatest example of God using evil for good is the death of Christ. Evil people brought him to the cross, but God used that cross as the means to save the world.