Not all Muslims hate Christians, in fact on at least two occasions (the Hapsburg Valois War and the Crimean War) Islamic nations allied with Christian European nations against other Christian European nations. There has been, however, a deep distrust between the two religions that has been exacerbated by historic events. A tremendous amount of resentment resulted from the First Crusade, when Christian soldiers slaughtered Islamic men, women and children wholesale. So many were killed that the horses of the knights lost their footing in the blood. President George W. Bush made the mistake of identifying the war on terrorism as a "crusade." Osama bin Laden picked up on this immediately and has frequently referred to the U.S. as "Crusader America."
United States support of Israel has also been an issue; as it is now the Palestinian people--who were in the land before the Jews--have been dispossessed. Their occupation of the land predates the occupation spoken of in the Old Testament. Palestine literally is "land of the Philistines." They believe history is on their side, and the U.S. support of Israel supplants that history.
Finally, there is the fact that Muslims consider Christianity an imperfect religion. They believe that the world rejected the message of God sent by Jesus, so God sent another prophet, Muhammad, as the last true messenger. Since Christians do not accept Muhammad and his teaching, the belief is that the Christian religion is incomplete, somewhat similar to Christian attitudes about Judaism.