Including Islam within the fold of traditional western religious tolerance is not business-as-usual. It is an experiment. Our Lockean ideas of religious tolerance had their origins in the 16th century (the peace of Augsburg) and the 17th (the peace of Westphalia).
In other words, "our Lockean ideas of religious tolerance" coincided with the emergence of an institution that would displace religion at center stage in human affairs. For example, Judeo-Christian orthodoxy became a lot less important to people when industrialists began scheduling work on Sundays. Given the choice between sustenance and faith, human beings become much more flexible about faith!
The purported conflict between "Islam" and "the West" is really just a conflict between the contending forms of economic organization these terms can imply. The same held for "communism" and "free-market enterprise" -- that is, until communism proved amenable to the latter, as in the contemporary case of China.
Western investors are enormously "tolerant" of anything that makes them richer, just as they display the most principled objections to anything that does not. In this way, identifying our friends and foes on the world stage is more readily accomplished than by employing any other criteria.