I was thinking earlier today about the juxtapositions of Saddam Hussein and Joseph Stalin, and how the communists in the Soviet Union loathed religion and, for a while, oppressed it. Can you imagine of Saddam Hussein practiced state atheism and today ~1/3 of the country was atheist? I don't think the region would know what to do with itself.
I don't think religion plays a large personal role for the leaders of these movements, it's merely the perfect tool for them to get the masses to impose their will. A lot of Muslim writers say that's the gist of it. I believe Reza Aslan (I'm a fan) talks about this often, that it's a political war using religious motivations.
I'm of the opinion that it's both, that Islam is both in a bit of a reformation and that the Middle East is literally in a reformation, tearing up the European-drawn map and changing boundaries to fit ethnic groups.
It's worth noting that, while the men you mentioned were certainly not champions of organized religion, they were also VERY irrational people. I don't think it's fair to assume that because they were against organized religion, the region would not have been better off for recognizing a false god.
Many people still beleive that religious conflict is caused by lack of education, poverty or by politics. I don't know where you stand in regards to religious belief, but I think you may be underestimating what it is like to be certain of paradise. Remember that the 9/11 hijackers were college educated, middle class people, with no discernable experience of political, social or economical oppression.They did, however, spend a large amount of time at their local mosque talking about the depravity of infadels and the pleasures that await marters in paradise.
How many more people must crash into buildings at 400 miles per hour or be murdered before we admit to ourselves that jihadist/Islamic violence is not a matter of education, poverty, politics or a struggle for power?