This is a good post and I think I need to refine my take a bit. While the official, state-sponsored version of Islam in many Arab, Gulf, and South Asian states provides a scaffolding of intolerance and hatred for other faiths and minorities, it stops short at providing the motives and encouragement to actually become a militant or terrorist.
Pakistan is a bit of a special example in that it is more willing to play with the hot stove of terrorism that most Gulf states have abandoned and views militant networks in Afghanistan and India as strategic assets even as it fights its own Pakistani Taliban. It is worth noting that the harshest forms of official Pakistani prejudice are aimed at unsatisfactory Muslims: the “apostate” Ahmadi and to a lesser extent the suspiciously tolerant Ismaili.
But in all cases, state-sanctioned Islam, even of the extreme conservative bent, pulls up short of encouraging the type of nihilistic militancy of ISIS or AQ, for good reason: these groups have extreme hostility to the governments that don’t walk the walk and are pragmatic when dealing with the kaffir great powers. And proponents of ISIS-style militant Islam are not long for the world in places where an official Islam exists.
Which leads to an odd situation where the most fertile recruiting and proselytizing zones for nihilistic militant Islam are in places where state power has completely collapsed OR inside of open, tolerant, secular Western democracies. They are uniquely unsuited for combatting it, and the paradox of tolerance absolutely comes into play. People would be jailed in Saudi or the UAE for delivering the types of Friday sermons heard weekly in Molenbeek. The most effective ISIS recruiter was an Australian convert who the Aussies struggled to jail until he finally followed through on his calls for jihad and tried to stage an uprising in the Philippines. And, Western authorities lack the nuance and community ties to differentiate between bog-standard conservative Islam (which presents its own issues to a pluralistic society) and the far more acutely dangerous explodey militant version.
The great majority of Muslims, even devout or conservative Muslims in the West will do what most people of all faiths do, which is find ways to accommodate deeply held religious sensibilities with their new surroundings and norms. A much smaller number will be unable to do so, and will in fact be further inflamed because in this ideological worldview it is a humiliation for Muslims to be forced to seek material prosperity among non-believers.
It is very difficult for Western nations to tackle this issue, not in the least because unhelpful rhetoric about civilizational clashes with all Muslims in the West and calls for absurd crackdowns clashes with equally unhelpful allegations of Islamophobia and racism when a more targeted and sensible approach is being sorted out.