Summary: An attempt to understand the incidents on September 11, 2001 based on the understanding of how the will of God works.
It is possible that all of us asked this question. No one should be blamed for asking it either. It was not an expression of unbelief. Just a cry from the pit of our hearts.
The answer to this touchy substance is in understanding how the will of God functions. This article is a meager attempt to define this in understandable terms.
Many of us had the misfortune to witness the tragedies of September 11, 2001 unfold right before our eyes on TV. There is no doubt that we will not be the same again. That day we realized that evil could sink to lower levels than we earlier thought possible. Many have turned to God as a result of this and will increase their faith. Many, especially who lost loved ones, will ultimately blame God for the evil and may lose whatever rudimentary faith they had.
Where was God on September 11th? Well, He was on His throne! These incidents did not happen in His absence. Neither was it a situation like the one Elijah alleged in 1 Kings 18 (quickview)  to prophets of Baal and Asherah. Nothing escapes the attention of God. “Our God is in heaven; He does whatever He pleases.” (Ps. 115:3). “The eyes of the Lord are in every place. Keeping watch on the evil and the good.” (Proverbs 15:3 (quickview) ). Even more astounding is the statement in Proverbs 16:4 (quickview) . “The Lord has made all for Himself. Yes, even the wicked for the day of doom.” This statement may trouble many. Did God create Mohammad Atta? Yes, He did! Does God agree with what He did? No! But He allowed it to happen. Was it according to God’s will that these tragedies happened? Well, yes and no. Let me explain.
When we study theology, we see that there are three areas to God’s will: the directive will of God, the perceptive will of God and the permissive will of God. The directive will of God is that by which God decrees what will come to pass. He stands in the background and directs everything that happens in this universe. This is done ‘according to His good pleasure which He purposed in Himself’ (Eph. 1:9), ‘according to the good pleasure of His will’ (Eph. 1:5) and ‘according to the counsel of His will’ (Eph. 1:11). It means that the directive will of God functions according to the counsel of His will, independent of any input from creation and that He does everything for His good pleasure or to bring glory to His name. This part of God’s will is hidden from us. So many things are happening all around us in the universe- black holes forming, stars being born, supernovas exploding etc. But we do not know about it. God knows about all of it and He is directing it.
Deuteronomy 29:29 (quickview)  is a key verse in understanding this. It clearly divides the will of God into two areas. “The secret things belong to the Lord our God, but those things which are revealed belong to us and to our children forever, that we may do all the words of this law.” The ‘secret things’ is the directive will of God. The ‘things revealed’ is the perceptive will of God. We should not worry about the ‘secret things’ because God has revealed enough things to us to equip us to live in a God glorifying way. God has revealed Himself through creation (Ps. 19:1, Rom. 1:19,20), thorough prophets (Heb. 1:1) and finally through His Son (Heb. 1:2,3).