There were Jewish communities, some quite large, throughout Europe and the Middle East before the Crusades. They had established themselves and survived over the course of many centuries, but they also provided tempting targets for marauding Crusaders looking for infidels to attack and treasure to loot. Caught between two warring religions, the Jews were in a most untenable position.
Christian antisemitism obviously existed long before the Crusades, but poor relations between Muslims and Christians served to exacerbate what was already a troubled situation. In 1009 Caliph Al-Hakim bi-Amr Allah, sixth Fatimid Caliph in Egypt and later the founder of the Druze sect, ordered the Holy Sepulchre and all Christian buildings in Jerusalem be destroyed. In 1012 he ordered all Christian and Jewish houses of worship destroyed.
One would think that this would have simply worsened relations between Muslims and Christians, despite the fact that Amr Allah was also considered mad and Muslims contributed heavily to the rebuilding of the Holy Sepulchre later on. For some reason, however, Jews were also blamed for these events.
In Europe a rumor developed that a Prince of Babylon had ordered the destruction of the Holy Sepulchre at the instigation of the Jews. Attacks on Jewish communities in cities like Rouen, Orelans, and Mainz ensued and this rumor helped lay the basis for later massacres of Jewish communities by Crusaders marching to the Holy Land.
One should not be misled into thinking that all of Christendom was united in violence against the Jews - it isn't even true that church leaders were so united. There was, instead, a wide variety of attitudes. Some hated the Jews; saw them as infidels, and concluded that since they were marching off to kill other infidels, why not get a head start with some locals. Others, however, wished the Jews no harm and sought to protect them.
This latter group included many churchmen. A few were successful in protecting local Jews from marauding Crusaders and managed to enlist the aid of local families to hide them. Others started out trying to help but gave in to the mobs lest they be killed as well. The archbishop of Mainz changed is mind a bit too slowly and had the flee the city in order to save his own life - but at least a thousand Jews weren't so lucky.
Of course, Christianity had for centuries been promoting vile images and attitudes about Jews - it's not as though this anti-Judaism came out of nowhere, springing fully-formed from the Crusaders' swords and spears. Thus, even a sympathetic consideration of the position in which the priests and bishops found themselves must conclude that they brought it themselves. Through action or inaction, the church encouraged treating Jews as second-class citizens, and this led quite readily towards treating them as less than human in the end.
There is no way to tell how many Jews died in Europe and the Holy Land at the hands of Christian Crusaders, but most estimates put the numbers at several tens of thousands. Sometimes they were offered the choice of baptism first (conversion or the sword is an image more commonly attributed to Muslim conquests, but Christians did it as well), but more often they were simply killed outright.
Quite a few others chose to determine their own fates rather than wait for the tender mercies of their Christian neighbors. In an act called kiddush ha-Shem, Jewish men would first kill their wives and children and then themselves - a form of voluntary martyrdom at their own hands. Ultimately the Jewish communities in Europe and the Middle East were the biggest losers to come out of the Christian Crusades against Islam.