I agree that fundamentalism is a problem. But I also agree that outside interference in the region has greatly increased fundamentalism in the region. It is not just some natural evolution of Islam.
So your comment here echoes the key concluding point of the article that I disagreed with
from the 2nd to last line of the OP quote said:
Illiberality and intolerance are intrinsic elements of Muslim doctrine, they argue
They key is to distinguish religion, theism, and Islam, from the variety of ideas, values and actions by every person who claims to adhere to religion, theism, or Islam.
Fundamentally, meaning at its core, the most central ideas of Islam and all Abrahamic monotheism are inherently at odds with liberalism, tolerance, progress, reasoned thought, and other such defining features of what is labeled "fundamentalist religion" which is really just religion when taken seriously and allowed to have influence.
The defining feature of God is the ultimate authority, thus the worship of him is the worship of authoritarian values which objectively impede the values of liberalism, liberty, and tolerance. This God and other foundational notions like an afterlife cannot be accepted without faith which is why all religions that take God's existence seriously promote the epistemology of faith which is definitionally the opposite of honest and reasoned thought.
US foreign policy has had an impact, but not in making Islam something that it isn't, but rather in fueling the influence of Islam's defining ideas and values upon those societies, impeding the kind of secularization that has happened in the West, which really amounts to people becoming less religious and taking religious ideas and values less seriously, even if they continue to con themselves that they are still "Christian" despite not treating the Bible with any more deference than they do Moby Dick.
Like Christianity was in the West, the ideas and values of Islam are a fundamental problem. Liberalism and tolerance occur in "Muslim" countries only when Islam is gutted of its influence and the words "Islam" and "Allah" are largely empty ceremonial pretense as Christianity is for most Westerners, except of course for "fundamentalist" who just those that take their religious ideas seriously and are authoritarian, intolerant, unreasonable, and anti-progressive as a result.