If we reject God's sovereignty over all things, then we tie His hands and make him subject to the will of man. This places man equal with God and that cannot be true.
God accomplishes His will in two ways. He acts immediately, through His direct Hand. He also acts through secondary causes, often using the instrumentality of men.
If wicked men are used, it is often said that God is the author of sin. This is blasphemous. God used sinful men to nail the Lord, who knew no sin, to the cross. Was the crucifixion a wicked act? Absolutely. Were the Roman soldiers and Pharisees responsible? Absolutely. Were they free to refuse to participate in this wicked act? Yes. Was the crucifixion outside of the will of God? Not all, for without it man could not be saved. Therefore, God is absolutely sovereign. At the same time, evil men were righteously held responsible. In the end, God was glorified and salvation wrought for sinners.
I have asked myself so often these last days "why?" I cannot say with certainty. I know that it would not have happened without God's permission. I know that God is not the author of evil. On the other hand, I do not know what it was supposed to mean.
All the affliction that faces mankind is a result of sin. The terrible things that befall us are the result of our sin. The horrenous events of the last week are the result of man's sin. Christ came to pay the debt of that sin for those he came to save. That is what makes his death so precious. All that being said, it is sophomoric and facile to say that these atrocities are the direct result of our national sins. That is entirely too convenient. On the other hand, we as a nation would be foolish not to be chastened and led to repent for our great wickedness. No doubt we as a nation have permitted great wickedness in our land. This should humble us and cause us to cry out to God for forgiveness and mercy.
By the same token, I am a great sinner too and have committed much wickedness. I may not have sanctioned the national sins of abortion or homosexulaity, but I have failed to love God or my neighbor as I ought. It would be foolish for me not to be chastened and to remain in a stiff-necked condition.
The people who died on the planes, in the WTC, and in the Pentagon never thought that Tuesday would be the end of their world. For the victims of these atrocities, the Bible offers the promise of eternal life to those that died in Christ. The moments of terror have been obliterated by the rapture of heaven. Those that died outside of Christ will spend eternity in unspeakable torment.
For those of us that remain, this truth offers great hope and comfort to the Christian. It also should cause the Christian to examine his life for the fruits of grace and whether or not we actually have a desire to walk in the will of God. On the other hand, it is indeed an alarm to the unconverted and reveals that God is mercifully providing the opportunity to repent and lean on Him.
In that regard, these events occurred not for the sins of those in the planes or in the buildings, however, it will result in God receiving all glory and honor.
I form the light, and create darkness: I make peace, and create evil: I the LORD do all these things. - Isaiah 45:7