I don't think you have any idea how Al Qaeda functions. The greater threat is the Muslim Brotherhood... Al Qaeda is kind of like the Ford Foundation of terror... it writes the checks... the causes emerge without the organization's interference... rarely they are commissioned based on particular goals (still rare).

So that brings us to how these causes come up... usually they emerge in societies (such as Egypt, Saudi Arabia, and Yemen) where repressive (often pro-Western dictators) eliminate all moderate opposition leaving only the most militant voices to challenge the status quo. In these environments, small, regional groups emerge and are funded and trained to cause upheaval or change.

In almost every case, their cause is nationalistic and not religious... they do, however, seek religious sanction and in turn promise to reform their territory under their patron's ideology (usually a salafi, deobandi, or wahabi interpretation).

In summary, it isn't the rise of Islam thats at fault but the rise of unchallenged, oppressive dictatorships.