Nowadays, it is often taken for granted that Muslims are staunch Anti-Semites. Most people in the West either do not know, or deliberately ignore, historical facts to the contrary.
History of Jews in Muslim Lands
Compared to Europe, Jews faired much better in Muslim lands over 1300+ years.
Even after conspiring against the nascent Muslim state in Madina, Prophet Muhammad allowed most of Jews to remain inside that state. The Jews remained in the oasis of Khaybar till long after his death. The prophet's own armor was with a Jew as collateral for money he borrowed.
When the Khaybar Jews were deported after an incident involving the beating of Caliph Omar's son, they were deported inside Muslim lands in Al-Sham (Syria/Palestine).
Jewish scholars flourish in Muslim Lands
Many Jewish scholars flourished under Muslim rule in Spain, Morocco, Tunisia, Cairo, Damascus and Baghdad. These include highly respected and learned figures such as Yaqub ibn Killis, Saadia Gaon, Issac Alfasi, Issac ibn Ghiyyat, Ibn Gabirol, Abraham and Moses ben Ezra, Samuel Ha-Nagid, Joseph ibn Migas, David ben Marwan al-Mekamez, Yehuda Halevi, Bahya ibn Paquda, Maimonides, Joseph ben Judah, Al-Harizi, and even Ibn Kammuna, among countless others.
Jews holding high offices
Many Jews held high positions, including court physicians, merchants, and even viziers in several states from east to west. Among them are Ibn Killis in Egypt, Samuel Ha-Nagid, his son Joseph Naghrela in Cordoba.
When the Jews were expelled from Spain and Portugal, they found refuge in lands controlled by the Ottoman Empire, giving rise to the Sephardi Jewish culture. Another segment of Jews are the Mizrahis, who existed in Muslim land before that Iberian expulsion.
Occasional persecution and pogroms
This is not to say that all was rosy all the time. There were occasions of forced conversions, e.g. under the puritan Almohades in the Maghreb, and under Al-Hakem, the eccenric ruler of Fatimid Egypt. However, these rulers made everyone under them suffer, and the conversions were repealed a few years later, as they are not from sincere conviction. Occasional pogroms did happen, but were rare. The most famous is when Joseph Nagrela (Samuel Ha-Nagid's son) was vizier of the berber Ibn Badis. Berber soldiers resented Joseph's influence and a mob of them attacked the palace and killed Joseph.
Those events were rare, and when they happened, they were part of wider conflicts, such as civil unrest, or general oppression for all.
Establishment of the State of Israel
The Palestinian-Israeli conflict in the 20th century changed the attitude towards Jews in the Arab world and Muslims in general. Israel and Judaism are often mixed together in a political conflict about land. Land that is sacred for all three Abrahamic faiths that is.
Alliance with Nazis and Axis
Between World War I and World War II, most Arab states allied themselves with the Nazis and the Axis powers. The reason is not simply anti-Semetism, but rather a resentment to the British occupation by allying with their enemies. There was hope that the Axis would win and hence Arab lands would overthrow the British occupation (in Egypt, Palestine, and Iraq).
Several scholars have pointed out that the current political conflict is with Israel and Zionist ideology. That is separate from Judaism, which has co-existed with Muslims and Christians in the region for a long time.
Two contemporary Western scholars have written recent articles on the topic. Swiss scholar Tariq Ramadan Muslims and Anti-Semitism an op-ed in the French Le Monde. American scholar, Hamza Yusuf wrote Holocaust denial undermines Islam, published in Tikkun, a progressive Jewish web site by Rabbi Lerner.