The whole ordeal of why we went into Afghanistan in the first place is a contested concept. There are many "theories" as to why we went in, the most accepted was being what HopeHacker mentioned.
However, we cannot forget that we went in there shortly after 9/11. The idea was if we break up the Taliban, then we break up Al Qaeda and other possible plotting terrorists. The old "Divide and Conquer" theory.
And yes, it is a religious war to some of them. The theory on why Osama bin Laden "turned" on us (remember we helped him out during the Cold War and supplied him with weapons to fight the Soviets out of Chechnya?) is because in 1990 non-muslims -the U.S.- stationed themselves on Saudi or muslim soil. To him this was an act of Holy War. That is why the 1993 bombings of the WTC and the 2001 tragedy occurred.
I would hesitate to listen to the media as they are nothing but pretty faces that are reading a teleprompter. They report the stuff that we "want" to hear. Ever notice now how the term "terrorist" is now being replaced with "fighter".
Heck now the media is saying that Hezbuhllah is winning the war on Isreal. after the August attacks, now suddenly they're winning? It's all propoganda.
Oh and pay no attention to Michael Moore either. He's just a bitter guy from Michigan.
We probably would have gone into Iraq with or without 9/11 happening.
Anyway, to go back to your question though Jamie, there's an article written by Samuel P. Huntington called the The Clash of the Civilizations
. Its lengthy, but a good read about the differences between them and us. The article (its now a book too) talks about how a lot of countries are returning to their root and rejecting a lot of western modernization in culture and being dependant on the west world. The article is good, well thought out and non-biased.