I am trying to understand the rise of militant Islam and from the little I've read, it seems that the problem is not with mainstream Islam per se, but with the Wahabi cult.
The Wahabi cult originated in the mid eighteenth century and its doctrine is taken from the Kitab al-Tawhid, a work that was considered, extreme and unIslamic in its day. Its writer was forced to flee into exile. He found a patron in Muhammad Al-Saud, whose decedents ended up ruling Saudi Arabia.
The Wahabi's caused continuous headaches for the British in the Northwest Frontier, but they were not recognised as a single movement, with various incidents being put down to the work of individual fanatics. They were fanatics all right, but there seems have been some method to the madness.
In more recent times, following the discovery of oil in Saudi Arabia and its subsequent independence, it appears that the Saudi's are taking the cult, or at least parts of it, to the mainstream.
There is a good article on the subject here and I am also working my way through Charles Allen's God's Terrorists, which is very well written. I have not yet finished the book and I don't enough on the subject to assess it, but its a fascinating read, have a look at the Amazon reviews on the same link.
To try and put things in context, I have also just picked up Angelo Rasanayagam's Modern History of Afghanistan, another very readable book.
This is not intended to stir up controversy, just an attempt to understand, would welcome comments on this, especially from Muslims.