I am curious why you are so dismissive of imperialism or colonialism as a set of causes.
There are a number of different phenomena in play, here. We can look at different events in the world, (not limited to Islam):
When we examine the Enlightenment, we can go back the the Renaissance for its seed ground. While Europe always had warring factions, there was general stability under the religious “empire” of the church. In fact, just prior to (and providing impetus to) the Renaissance, there were a number of different movements within the church that showed more ecumenical and liberal ideals than had existed, previously. However, when some of those ideas threatened the “empire” of the church, the church withdrew to its most conservative positions, attempting to quash all such movements. The resulting Reformation and Counter-Reformation battles that neither side could win provided a basis for the development of secular thought. (It is all fine and well to hold a strict religious belief, but a secular approach allows one to work with religious “enemies” to promote trade or to form alliances with those “enemies” against others–even others who might be on the same side of the religious feuds.)
So secularism began to get a toehold in Europe.
Meanwhile, the various factors that led to the Reformation, (recent availability of large numbers of Greek and Hebrew texts that allowed people to challenge the official Latin version of scripture, vast holdings of property by the church, temporal power held by the church that provoked and promoted interference by the church with civil authority and interference by civil authority with the church, etc.), did not occur in Muslim lands, as there was no “church” to engage.
Europe’s sea borne adventures took Europeans to nearly all the globe, typically resulting in interference with local societies. From the sixteenth through the early 20th centuries, Europeans exerted increasing control over India, Indonesia, Philippines, then Egypt and Sudan, Algeria, Morocco, with attempts at Afghanistan and other locations. Following WWI, with the defeat of the aging Ottoman empire, Europeans chopped up the Middle East in ways that disrupted traditional tribal boundaries.
Meanwhile, in the nineteenth century, a conservative movement, Salafism, began in the Arabian peninsula that provided a rallying point for people upset about foreign control of their lands. The frequent reaction to this movement by the (European or European influenced) governments was fear accompanied by suppression. This gave status to the Salafist groups as freedom fighters, as well as strengthening the groups and making them more conservative (as persecution generally does).
The Cold War kept some of those groups contained, and provided more persecution to encourage proselytizing and conservatism: The Shah’s anti-Islam laws, the treatment of Filipino Muslims as “communists,” the suppression of Islamic culture in Indonesia, (again the laws were couched in “anti-communist” terms), the Soviet suppression of Chechnya, the Soviet invasion of Afghanistan, and other events. As the Cold War wound down, the major powers turned their attention away from their proxy wars and the Salafists were able to promote their beliefs as a combination of indigenous freedom fighting and a return to “real” Islam (although Salafism is only one of many movements within Islam). Thus, the most extreme of the Mujahideen supported by Reagan and Bush were able to re-form as the Taliban, and eventually conquer Afghanistan, protests against the Shah’s anti-Islamic laws allowed the Ayatollah Khomeini to establish a theocracy in Iran, bin Laden, angered by what he considered the irreverence and corruption of the House of Saud created al Qaida and then turned his attention against the U.S. that had propped up that family.
Of course, amidst these many movements and conflicts, it was hardly surprising that Abu Musab al-Zarqawi and Abu Omar al-Baghdadi could come up with the idea of “retoring” the Caliphate and creating ISIS, (much as Pol Pot and his Khmer Rouge established a brutal regime based on a “pure” Maoist Marxism that had little to nothing to do with the actual ideas of Karl Marx).
So, European (and later, American), interference in their countries played a strong role in providing the Salafists the opportunity to proselytize their particular version of Islam across the world. Very few Salafist groups are purely religious. Pretty much every one of them has its origins in rebellion against attempts to suppress either the religious beliefs or the desire for self-government of the people.
