There is quite a difference between 1000 and 1400, logically and statistically.
I think Islamic extremism is more reactionary to external influences (protecting their religious and political freedom), whereas the crusades were an attempt to force the religion upon others and continue to manipulate power. Keep in mind also that the original crusades were often targeted specifically AT muslims, so it is easier to sympathize with the reaction from Islam than it is the instigation from Christianity. This is not to say that such warring did not occur prior to the crusades (in fact, the first Crusade was a reaction to an insurgence of Islam); rather, Christianity greatly escalated the problem.