Well when a regime's legitimacy is predicated on not just providing for the defense of the two holiest cities of Islam, but upholding the ultra-puritanical strain of Islam known as Wahhabism (remember, the alliance between the House of Saud and the Wahhabi clerics dates back to the 1700s, IIRC), and when said regime has systematically eliminated (or attempted to eliminate, anyway) any and all threats to their rule - as well as dissenting views from the ruling Wahhabi orthodoxy; and when that regime reveals itself to be not just in strategic alliance with the Western infidels, but incredibly corrupt and hypocritical in the behavior of its own rulers (e.g., the lavish, Westernized lifestyles of many Saudi royals and other elite businessmen), is it any surprise that many Saudi citizens will grow frustrated and angry with both the hypocritical, corrupt, and absolutist dictators that rule their country, as well as the "Great Satan" of the United States and other Western countries that ally with the House of Saud?
Under the particular conditions of the Kingdom of Saudi Arabia - a population deeply indoctrinated in Wahhabi ideology, no civil society to speak of (other than rabidly Wahhabist mosques), and prospects for economic advancement being few and far between - the potential for an uprising is dangerously high. But such an uprising, far from being a remotely secular, liberal, or democratic revolution, would be an even more aggressively - and violently - Wahhabist, and openly anti-Western, in alignment with the likes of al-Qaeda, al-Nusra, and ISIS.
Given these conditions, the inclination of the House of Saud has not been to liberalize or introduce substantive reforms, but to export the Kingdom's ruling Wahhabism all over the world. This serves two functions: first, it keeps the home-grown Saudi jihadists away from the Kingdom, where they are no longer an immediate threat to the ruling family. Second, it shores up the legitimacy of the House of Saud in the eyes of both the Wahhabist clerics - who are incredibly influential within Saudi society - as well as many devout Sunni Muslims around the world, who have increasingly looked to Wahhabism as the standard by which all Muslims ought to be measured.
Thus, it does not surprise me in the slightest that members of the House of Saud, other Saudi government officials (perhaps especially in the military as well as the intelligence and foreign affairs services), Saudi "charities" that were easily infiltrated by operatives from Al-Qaeda and other jihadist organizations), and fabulously wealthy Saudi businessmen have donated generous sums of money over the years to all kinds of Wahhabist (or Wahhabi-influenced) individuals and organizations. And it does not surprise me at all that some of that money ended up in the hands of the 9/11 hijackers.
The real scandal here is the fact that the U.S. government has been allied for so long with this brutally dictatorial regime that has cynically exported the ideology and the organizations that have directly given rise to the most dangerous terrorist organizations in the world.