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This is a ridiculous question. Why does God let anything bad happen at all? Why did God allow the Civil War, WWI, WWII, the Korean War and Vietnam to happen? Is every bit of human strife due to God punishing us? What did the Afghan peasants do to deserve a life a pain, suffering, oppression and starvation? Why does a child deserve to grow up in a fly infested poverty-stricken culture? When you can answer these questions and more then you can answer why God let 9/11 happen.

Of course, God does allow many evil things to happen. Like abortion, murder, rape, genocide. The question is not "Why does God allow it?". The question is "Is it His will?". The answer to all questions of evil is of course it is not His will. But, He has given man free will of our own so that we may choose to have a relationship with Him not based on His punishing us into doing things to please Him, but based on the knowledge that He loves us and poured out the wrath of His justice upon His own Son, so we could choose to love Him without condemnation or fear of punishment. It says in the Bible that it is His kindness that leads men to repentance. Not punishment.

The question of "Why did God let xxxx happen?", where the "xxxx" can be any tragedy great or small, has been one for the ages. The answer, to anyone who knows God through His Word is pretty straightforward, and very logical.

God gave man both breath and freedom in the Garden of Eden. Man was not made a robot, but had the free will to decide his own course.
Man chose sin, and the consequences were chaos, and death. (Note: Adam chose sin, but every man and woman (a) would do the same, and (b) has sinned at least once in their lives. All mankind is sinful.)
The entire universe has been dying since the first sin. Nothing has been quite "right" in God's creation since the first sin. Neither natural calamities (e.g. earthquakes, storms, floods, etc.) nor human tragedy (let alone murder and war) was any part of God's plan. Mankind, with the malevolent support of Satan, created the evil in this world independent of God.
God did interject Himself into this dying world to save mankind, in the only way possible to "right" the original wrong (multiplied by the sins of billions), by sending His Son Jesus to (a) pay our price, and (b) create life in a dying world.
Men and women still have free will. We can continue to sin and die forever, or we can kneel at the cross of Christ, commit our souls to Jesus as Lord and Savior, and receive both forgiveness and adoption into God's family.
God has said in His Word that the evil of this world will exist, but not forever. Christ will return to judge and separate the wicked from God's family, and create a new heaven and new earth, devoid of the chaos that sin has wrought.

It is indeed ironic that so many who will not acknowledge or respect God will immediately blame Him for every evil in this world. September 11 was God's fault? Any objective person can see that such twisted logic comes only from the Liar himself, the author of evil, Satan.

God is GOOD! Satan is evil! God grants true FREEDOM, while Satan offers men and women Taliban-like bondage. Unfortunately, both good and evil people on this earth have the same freedom to sin, and that sin has consequences that effects both innocents and the wicked.