Saying Jews were on one side or the other doesn't give this question the right answer. The Jews were not one defined nation and instead lived throughout the Middle East, North Africa, and Europe. During the first Crusade there were some instances of Jews and Muslims defending Haifa, Jerusalem and Ramlah together, even to the point where Jews and Muslims died side by side during the massacre of Jerusalem. Muslims would also attack Crusaders that had enslaved Jews and set them free. Jews in Europe suffered from a massive rise in anti-semitism during the Crusades. During the Rhineland March, mobs of French and German soldiers looted and destroyed Jewish villages and many Jews elsewhere were ostracized from society. These attacks were not endorsed by leaders, but still happened frequently to the point where Holy Roman Emperor Henry IV issued a ban on these attacks. One could argue being a Jew in Europe was worse than being a Jew in the Seljuk (Turkish) Empire. In conclusion, the Jews would have favored being under Muslim rule rather than European rule, but not because they liked being under the Muslims (they were still heavily taxed and not allowed in certain professions), more because the Muslims 'beat them with a smaller stick'.