1) Reading the Koran /= Studying Islam in an academic or religious setting. All religions except scientology are based on ancient and arguably obsolete texts, and to understand the religion, you have to understand how it's interpreted by different people.
2) The rise of fundamentalism has very little to with the particular religion itself. It's about globalization of culture polarizing people to a sometimes extreme (or even idealized/hypothetical) set of values as a reaction to the changing world. The Arab world has changed a lot more in the last 60 years than it had in several hundred prior, at least as far as the average man is concerned, and some people are scared by this.
So it's not that they look at the religion and come to this conclusion, it's that they're craving something "ancient" and "traditional" and they use religious texts to fill that role and interpret them in a way convenient to their anxieties.
Case in point, it's reproducable in other religions. Both Christianity and Judaism have seen an increasing number of fundamentalists in America, and that's without the foreign element introduced. Granted they haven't been largely violent, but believe me if the changes in this country were as dramatic as the ones in the middle east, they would.

