In 1001 AD the Western church divided between the Roman Catholic Church and Eastern Orthodox Church. There were many reasons for the split, but one cause was the filioque. According to the Wikipedia —
Filioque, Latin for “and (from) the Son”, was added in Western Christianity to the Nicene-Constantinopolitan Creed. This insertion emphasizes that Jesus, the Son, is of equal divinity with God, the Father, while the absence of it in Eastern Christianity emphasizes that the Father is the only one cause of the two other persons.
Et in Spiritum Sanctum, Dominum, et vivificantem: qui ex Patre Filioque procedit.
(And in the Holy Spirit, the Lord, and giver of life, who proceeds from the Father and the Son.)
The doctrine expressed by this phrase, as inserted into the Creed, is accepted by the Roman Catholic Church, by Anglicanism. and by Protestant churches in general. Christians of these groups generally include it when reciting the Nicene Creed. Nonetheless, these groups recognize that Filioque is not part of the original text established at the First Council of Constantinople in 381 and they do not demand that others too should use it when saying the Creed. Indeed, the Roman Catholic Church does not add the phrase corresponding to Filioque (??? ??? ????) to the Greek text of the Creed, even in the liturgy for Latin Rite Catholics. Pope John Paul II recited the Nicene Creed several times with patriarchs of the Eastern Orthodox Church in Greek according to the original text.
At the 879-880 Council of Constantinople the Eastern Orthodox Church anathematized the “Filioque” phrase, “as a novelty and augmentation of the Creed”, and in their 1848 encyclical the Eastern Patriarchs spoke of it as a heresy.
In 1054, the eastern and western churches split (the Great Schism) over this very issue — as well as over whether communion bread should be leavened or unleavened. As the Wikipedia describes it,
Patriarch Michael I ordered a letter to be written to the bishop of Trani in which he attacked the “Judaistic” practices of the West, namely the use of unleavened bread. The letter was to be sent by John to all the bishops of the West, including the Pope. …
In response to Michael’s refusal to address the issues at hand, the legatine mission took the extreme measure of entering the church of the Hagia Sophia during the divine liturgy and placing a Bull of Excommunication (1054) on the altar.
Protestants usually use unleavened bread, because that is certainly the bread Jesus used at the Passover when he initiated communion. And, some would argue, the lack of leaven would symbolize the purity of Christ — the perfect sacrifice. But the Orthodox Church used leavened bread and an Orthodox Patriarch accused the Western church of being “Judaistic.” Well, of course, Christianity is Judaistic, but by this time, the Jews were so hated that the church was working hard to expunge all memory of its Jewish roots.
Ultimately, the two halves of the church excommunicated each other. Excommunnication meant the Catholics didn’t see the Orthodox as Christians at all. Indeed, they soon saw them as people to be massacred.
During the Fourth Crusade, however, Latin crusaders and Venetian merchants sacked Constantinople, looting The Church of Holy Wisdom and various other Orthodox Holy sites and converting The Church of Holy Wisdom and other holy sites from Orthodox Christian sites to Roman Catholic ones. These churches’ and monasteries’ holy artifacts were taken to the West, and many of these artifacts have yet to be returned. This was proceeded by a European backed attempted conquest of Byzantium, Greece, and Bulgaria (see the Battle of Adrianople (1205)) and other “Eastern” Christian countries which led to the establishment of the Latin Empire of the East and the Latin Patriarch of Constantinople (with various other Crusader states). This period of chaotic rule over the sacked and looted lands of the Byzantine Empire is still known among Eastern Christians as Frangokratia. The sacking of Constantinople is also seen as a factor that weakened Byzantium and led to its to fall to Islam. Various crusades before and after targeted and massacred Orthodox Christians (see the Northern crusades for example). 
Regarding the Fourth Crusade,
Speros Vryonis in Byzantium and Europe gives a vivid account of the sack of Constantinople by the Frankish and Venetian Crusaders of the Fourth Crusade:
The Latin soldiery subjected the greatest city in Europe to an indescribable sack. For three days they murdered, raped, looted and destroyed on a scale which even the ancient Vandals and Goths would have found unbelievable. Constantinople had become a veritable museum of ancient and Byzantine art, an emporium of such incredible wealth that the Latins were astounded at the riches they found. Though the Venetians had an appreciation for the art which they discovered (they were themselves semi-Byzantines) and saved much of it, the French and others destroyed indiscriminately, halting to refresh themselves with wine, violation of nuns, and murder of Orthodox clerics. The Crusaders vented their hatred for the Greeks most spectacularly in the desecration of the greatest Church in Christendom. They smashed the silver iconostasis, the icons and the holy books of Hagia Sophia, and seated upon the patriarchal throne a whore who sang coarse songs as they drank wine from the Church’s holy vessels. The estrangement of East and West, which had proceeded over the centuries, culminated in the horrible massacre that accompanied the conquest of Constantinople. The Greeks were convinced that even the Turks, had they taken the city, would not have been as cruel as the Latin Christians. The defeat of Byzantium, already in a state of decline, accelerated political degeneration so that the Byzantines eventually became an easy prey to the Turks. The Crusading movement thus resulted, ultimately, in the victory of Islam, a result which was of course the exact opposite of its original intention.
Thus, we see an evolution from disagreement, to heretic, to subhuman. If heretics could be burned at the stake, why not murdered or raped?
Now, if you’ve ever wondered how the Holocaust could have happened in 20th Century Europe, don’t blame just Hitler. Blame also a corruption of Christianity that teaches it’s our job to hate and punish those who disagree with us. The Jews became subhuman for the same reasons the Orthodox and the Nestorians did.
The two founders of the Reformation were Luther and Zwingli. They had a common enemy in the Catholic Church, and both were at risk of being caught, tried, and burned at the stake. Soon, wars would be fought over their views. And so they made an effort to join cause and teach a common theology.
By spring 1527, Luther reacted strongly to Zwingli’s views in a treatise placing his disagreement with Zwingli in the context of a battle against Satanic forces. The controversy continued until 1528 when efforts to build bridges between the Lutheran and the Zwinglian views began. Martin Bucer tried to mediate while Philip of Hesse, who wanted to form a political coalition of all Protestant forces, invited the two parties to Marburg to discuss their differences. This event became known as the Marburg Colloquy.
Zwingli accepted Philip’s invitation fully believing that he would be able to convince Luther. By contrast, Luther did not expect anything to come out of the meeting and had to be urged by Philip to attend. Zwingli, accompanied by Oecolampadius, arrived on 28 September 1529 with Luther and Philipp Melanchthon arriving shortly thereafter. Other theologians also participated including Martin Bucer, Andreas Osiander, Johannes Brenz, and Justus Jonas. The debates were held from 1–3 October and the results were published in the fifteen Marburg Articles. The participants were able to agree on fourteen of the articles, but the fifteenth article established the differences in their views on the presence of Christ in the Eucharist. Afterwards, each side was convinced that they were the victors, but in fact the controversy was not resolved and the final result was the formation of two different Protestant confessions.
The result was not only a permanent split in Protestantism but a weakened Protestant effort.
Now, in many ways, Luther is a true hero of the faith, and we owe a lot to him. But he was also a raving anti-Semite — as was most of the rest of Europe.
In 1523, Luther advised kindness toward the Jews in That Jesus Christ was Born a Jew, but only with the aim of converting them to Christianity. When his efforts at conversion failed, he grew increasingly bitter toward them.
Luther’s other major works on the Jews were his 60,000-word treatise Von den Juden und Ihren Lügen (On the Jews and Their Lies), and Vom Schem Hamphoras und vom Geschlecht Christi (On the Holy Name and the Lineage of Christ), both published in 1543, three years before his death. Luther argued that the Jews were no longer the chosen people but “the devil’s people”: he referred to them with violent, vile language. Luther advocated setting synagogues on fire, destroying Jewish prayerbooks, forbidding rabbis from preaching, seizing Jews’ property and money, and smashing up their homes, so that these “poisonous envenomed worms” would be forced into labour or expelled “for all time”. In Robert Michael’s view, Luther’s words “We are at fault in not slaying them” amounted to a sanction of murder.
By the time of the Reformation, the “Christian” principle was simple: if you don’t agree with me, not only will you go to hell, you deserve to die painfully and slowly.