Hmm. I think that business about marginalization is just slightly off the mark. Here's my take on it.
Islam is a former Number One. Back in the Middle Ages, while Christian Europe sank into barbarism, the Muslim world presented a high civilization, advanced in art and science, wealthy and a great place to live. Not coincidentally, the Muslim world also far exceeded the West when it came to religious toleration. Although it fell short by modern standards, the fact remains that in Muslim countries non-Muslims could and did live unmolested and free to practice their religions or irreligions as they saw fit. (This is actually prescribed in the Quran, which shows once more that what's in the scripture doesn't determine the behavior of believers. When they are inclined to behave according to what the scriptures say anyway, they do and say they are doing it because that's what the scriptures say; when they aren't, they don't and the scriptures get ignored or explained away.)
Today, the secular West has surpassed the Muslim world in all of these areas and Muslims are afflicted with a collective sense of inferiority and deprivation. The desire to restore Islam to its former Number One status is natural, and so is confusion about how best to do that. Restoring the toleration and encouragement for learning that once characterized the Muslim world, and was the reason for its Number One status, is the way to do it. Committing acts of violence is not.
Unfortunately, the tendency to do that latter is quite human.