I don't think so. Jews were outcasts, not owning land--that's why they got the reputation as city-dwelling jewelers, doctors, and other urban professions. Muslims in Spain were driven back to North Africa in the 1200s.
Jews I think are a special case. That said, crusaders seeking to kill Jews in the Rhineland during the First Crusade did come up against opposition from the many Bishops in the area who gave them protection, notably the Bishop of Cologne. As for the Muslims, they were not driven back to North Africa until the fall of Grenada in
1492 following over two centuries of existence as a tributary kingdom of Castille. This status as a tributary kingdom was very much in the tradition of the Muslim lords who owed tribute to Christian Kings, and vice versa, in the earlier medieval period. There are plenty of examples that show to us that Spain was perhaps the most tolerant of different religions, seeing as muslim, christian and jew existed in relative harmony and cultural primacy, though decidely more so in the 10th century and in the Muslim side. It was by the beginning of the 16th Century that the last Muslims were either converted or exiled from Spain... and of course that leads onto the proposition that the Reformation was a far more intolerant time than any period before or after. Spanish Inquisition, Bartholomew's Day Masacre, 30 Years War, English Civil War...
Yet I'd rather give more examples of... not so much tolerance and everyone living side by side in harmony, but examples of the incredible variety that existed in medieval Europe. Always include the Byzantine and Islamic world in that, since we are all children of the Roman Empire (whether we like it or not). Norman ruled Southern Italy, though often embroiled in conflict, managed to have Muslims, Orthodox and Catholic Christians without one side genociding or converting the other. The presence of the Normans meant especially that, as outsiders, they had little interest in supporting one side over another.
After around three hundred years of Muslim rule, much of the "Holy Land", from Jerusalem to Antioch and Edessa, was in fact quite evenly mixed with Christians and Muslims. Of course there would be more Christians in Antioch than in Jerusalem, the stipulations of the Bishop of Jerusalem when it was conquered originally still held sway even after various mad Caliphs and oppressive Jews (who took advantage of the Sassanid war against Byzantium beforehand to massacre the Christians of the city) had their way with the populace. One Caliph of Egypt even had to make huge concessions to the Christians, whose churches he had all recently demolished the roofs of and then had rebuilt, because he had annoyed the Muslim population of his realm. That it was even considered as an alternative, and that his mother was a Christian, shows us that it was not a black and white division.
Christians were also learning from Muslim texts, who were learning from Christian and Pagan texts, before, during, and after the Crusades. These texts usually ranged from commentaries on classical sources to commentaries on the nature of god and faith itself.
Finally of course there are the huge number of heretics living rather peaceful lives, the existence of pagans in centres of monotheistic religiosity and the presence of incongrueties within the faiths themselves that give support to a theory that the Middle Ages were not as intolerant as popular imagery depicts. But this is not purely tolerance on the part of medieval people. In addition to values of tolerance in peace time, it helps a great deal that for most their religiosity and ethnicity were not defined in the same way they would be in another few hundred years. Christianity enforced a popular identity following their experiences with heretics in the middle ages, and with a need to identify themselves they clashed with those who were clearly
not what they were.
... and oh dear I went on a rant.
