When Mohammed died, the Christians and Jews of Arabia had been totally subjugated. The history of his relations with the Jews and Christians determined how they have been treated over the past 1400 years.
Every action and word that comes from Islam today starts with the Mohammed's perfect example. In the very beginning in Mecca, Mohammed said that his prophecies came via the angel, Gabriel, who was the one who spoke to Moses. In Mecca he presented himself as a prophet in the line of Jewish prophets. However, the Koran also talks about Judgment Day, a Christian concept. In essence Islam is both a Christian and Jewish heresy.
Later, in Medina Mohammed persecuted both Jews and Christians. Jihad destroyed the polytheists and subjugated both Jews and Christians. Islam has a dual nature in its dealings with the Jews and Christians. They are "brothers" in religion and they are mortal enemies to be destroyed. You cannot understand the jihad with Israel without knowing the Islamic doctrine of the Christians and Jews.