Did Muslims mistreat the non-Muslims under their rule?
Allah Almighty orders Muslims to treat the people of other faiths, as long as they do not fight the Muslims, with kindness and justice. See Quranic translation (60:7-8): “Allâh does not forbid you to deal justly and kindly with those who fought not against you on account of religion nor drove you out of your homes. Verily, Allâh loves those who deal with equity. (8) It is only as regards those who fought against you on account of religion, and have driven you out of your homes, and helped to drive you out, that Allâh forbids you to befriend them. And whosoever will befriend them, then such are the Zâlimûn (wrong-doers those who disobey Allâh).”
These verses and other teaching of the prophet peace be upon him are what taught Muslims to respect and tolerate people of other faiths, as long as they are not harming the Muslim community. Churches and Synagogues stand until today in most of the Muslim countries are a witness that the non-Muslims had religious freedom. Many Jews, and Christians held high ranking jobs in the Muslim government.
Historically, Omar Bin Al-Khattab, the second Guided Leader (Khalifa) after the Prophet (PBUH) who entered Jerusalem in 637, refused to pray in the middle of the Church of the Holy Sepulcher (aka Church of the Resurrection) in Jerusalem, and instead prayed on the side so as not to violate the church’s sanctity.
Despite an era of Muslim leaders during the Islamic decline many centuries after Omar Bin Al-Khattab, who did not respect that sanctity, the Church still stands today as a place of worship for Christians.