I think it had more to do with differing forms of treatments towards Jewish communities than any active protection on part of Muslims. Under both Muslim and Christian rule, Jews were minority communities and were protected for religious reasons. Under Muslims, Jews were considered People of the Book and were therefore allowed to live peacefully under Islamic rule as dhimmi groups paying jizya taxes. Under Christian rule, Jewish communities were protected because extant Jewish groups were necessary for the final conversion at the end of time. Thus, in both situations, Jews are "protected". Though not the theater the term "Crusades" conjures up in the mind of most, medieval Spain offers some of the most documented evidence of Jewish existence as a minority group in a society engaged in religious warfare (though exactly how much of the Crusades and the Spanish reconquista were truly driven by religious and cultural zeal is an entirely different discussion). In medieval Spain, Jewish communities under Muslim rule had some level of freedom of movement within society that was not present in Jewish groups under Christian rule. There's documentation of a number of Jewish individuals who were able to work their way up the administrative ladder under Muslim rule. Such cases of social mobility were far more limited in Christian controlled lands. However, in both cases Jews were still required by law to distinguish themselves from Christians and Muslims by the way they dressed and by where they lived. As for fighting, there is documentation of Jews fighting for Muslims against Christian armies; there are even some instances in which these armies were led by a Jewish official in the Muslim administration. However, there are equally as many examples of Christians fighting for Muslims against both Christian and Muslim opponents. In fact, it was quite common during this time period for fighters of one faith to actively fight for another faith for monetary or political gains. Of course, this also represents a larger theme of cultural and religious mixing that often occurred in lands containing all three major faiths. For more exact information on the treatment of the Jews under Muslim and Christian rule during the middle ages, I suggest (and pulled my answers from) the following texts:

Menocal, Maria Rosa. The Ornament of the World: How Muslims, Jews, and Christians Created a Culture of Tolerance in Medieval Spain. Boston: Back Bay Books / Little, Brown and Company, 2002.

Ray, Jonathan. The Sephardic Frontier: The Reconquista and the Jewish Community in Medieval Iberia. Ithaca, N.Y.: Cornell University Press, 2006.

Catlos, Brian A. The Victors and the Vanquished Christians and Muslims of Catalonia and Aragon, 1050-1300. Cambridge, UK: Cambridge University Press, 2004.

Brundage, James A. The Crusades: A Documentary Survey. Milwaukee, Wis.: Marquette University Press, 1962.

Hillenbrand, Carole. The Crusades: Islamic Perspectives. New York: Routledge, 2000.

Nirenberg, David. Communities of Violence: Persecution of Minorities in the Middle Ages. Princeton, N.J.: Princeton University Press, 1996.