Is Islam intolerant of other religious minorities?

Islam recognizes the rights of minorities. To ensure their welfare and safety, Muslim rulers initiated a tax (Jizia) on them. The Prophet forbade Muslim armies to destroy places of worship such as churches and synagogues. Caliph Umer did not even allow them to pray inside a church. Jews were welcomed and flourished in Muslim Spain and when they were persecuted in Spain the rest of Europe after the exit of Muslims, Turkey gave the Jews refuge. The Jews consider that part of their history as the Golden Era. In Muslim countries, Christians live in prosperity, hold government positions and attend their church. Pakistan has had a Christian chief justice of the Supreme Court. Even Iraq has a Christian senior vice president. Christian missionaries are allowed to establish and operate their churches, schools and hospitals. However, the same religious tolerance is not always available to Muslim minorities as seen in the past during Spanish Inquisition and the Crusades, or as seen now by the events in Bosnia, Israel and India. Muslims do recognize that sometimes the actions of a ruler do not reflect the teachings of his religion and in fact, many of the Muslims being accused of terrorism are struggling against such undemocratic regimes.