Islam is a nebulous and broad term. Essentially what you are doing is watching a film about the Christian problem of FLDS polygamists and snake handlers and expecting to to understand the Orthodox view of the Ecumenical Councils from said film.
I'm not so big into films, but as far as books go, a good primer on the creation of the modern political situation of much of the Near East:
A Peace to End All Peace: The Fall of the Ottoman Empire and the Creation of the Modern Middle East by David Fromkin
One very interesting and timely point Fromkin makes is that the British never quite understood how decentralised Islam is and thought that by manipulating a Caliphate they could placate their Indian Muslim subjects.
A good look at the creation of modern Jihad groups is Steve Coll's Ghost Wars. While is it sort of a side issue to the main focus, the Arab volunteers in the Afghan Jihad were misfits before they left to go fit and by the time they returned they were causing all sorts of trouble. Coll has another good book about the bin Laden family and the creation of Saudi Arabia.
If you are looking more specifically about terrorist type Islam, books dealing with the Wahhabists would be best. The Deobandi movement is the equivalent in South Asia. Contemporaneous but completely different as far as ideology goes was Jadidism among Turkic Muslims.
The point Coll makes about the Wahhabis in Saudi Arabia is the social contract of the kingdom is that the radicals can export it all they want so long as they don't cause domestic trouble. That's basically the root of your modern Sunni extremism.
The issue I take with a lot of the Western produced exposes on Islam is that they focus on this core group of Arab jihadists with the assumption that they are representative of everyone fighting under the banner of Islam. While I'd agree that Islam has played some ideological role in nearly every conflict (but perhaps not more so than Christianity does in the US in some cases) involving Muslims, to see them linked as a grand, organized, monolithic struggle against the kaffir just doesn't add up to me.