Churches, monasteries, and synagogues existed from the very first caliphate of Abu Bakr in 632 all the way through to the abolishment of the Ottoman caliphate in 1924. Sometimes favored, often persecuted, Christian communities existed and even flourished all throughout that period from the time of the Righteously Guided Caliphs that ISIS claims to follow and revere.
The relationship between Salafi jihadists groups and local Christian populations has been a complicated one. While Al-Qaeda has always exhorted jihadis to keep their focus on their main enemy in the U.S., local groups have often targeted religious minorities. Some of the Egyptian jihadist groups of the 1970s which eventually became part of Al-Qaeda focused particularly on killing and robbing Coptic Christians, and gave justifications for doing so that were very similar to those that ISIS would later use.
Still, as recently as September 2013, Al-Qaeda's Al-Sahab Media issued a document titled "General Guidelines for Jihad," in English, Arabic, and Urdu, which called for focusing on terrorism against the Crusader West but also for avoiding "meddling with Christian, Sikh and Hindu communities living in Muslim lands." Interestingly, it also called for avoiding "fighting the deviant sects such as Rawafidh [pejorative term for Shi'a], Ismailis, Qadianis, and deviant Sufis, except if they fight the Ahl Al-Sunnah." Of course, these guidelines were often ignored by Al-Qaeda franchises, and by September 2013, Al-Qaeda and ISIS had broken off relations and gone their separate ways.
Islamic State "Abolishes" Pact of Omar
Al-Qaeda in Iraq and its successor the Islamic State of Iraq (ISI) directed most of their sectarian focus on the Shi'a; however, as early as March 2007, the State's proto-caliph, "Commander of the Faithful" Abu Omar Al-Baghdadi (Hamid Al-Zawi) described Christians as fair game:
"We find that the sects of the People of the Book and others from the Sabians and so in the State of Islam today are people of war who qualify for no protection, for they have transgressed against whatever they agreed to in many countless ways, and if they want peace and security then they must start a new era with the State of Islam according to (Caliph) Omar's stipulations [the historic "Covenant" of Caliph Omar with Christians] that they have annulled."
As Iraq scholar Nibras Kazimi has noted, this first Al-Baghdadi laid claim to authority based on the implementation of an aggressive Salafi agenda which claimed to have transformed Iraq, in 2007, into "one of the greatest nations on the face of the earth in maintaining monotheism, for there is no polytheistic Sufism being propagated, or shrines being visited, or innovated festivals being celebrated, or candles being lit, or a pilgrimage being made to a pagan totem, for the people of Iraq have destroyed these shrines with their own hands so that Allah will be worshiped alone." Here then is the vividly illustrated Salafi agenda that ISIS would implement in Syria and Iraq as it took advantage of anarchy and dysfunction in large parts of both states.
Islamic State statements also blamed Arab Christians for promoting the concept of Arabism at the expense of Islam, an ironic charge given the claims about the role of Iraqi Baathists in the organization. Arab nationalism is, of course, a principle tenet of Ba'athism. Some months after that announcement, gunmen killed Chaldean Catholic priest Ragheed Aziz Ghanni and three of his deacons in Mosul after they refused to either close their church or convert to Islam. In February 2008, the Chaldean Catholic Archbishop of Mosul Msgr. Paulos Faraj Rahho was kidnapped and killed by Islamic State gunmen.
The general atmosphere of violence and insecurity in Iraq after the 2003 invasion meant that individuals of all faiths were kidnapped and killed, sometimes for motives that seemed less than clear. But Iraqi Christian sites were targeted early on, with six churches in Baghdad and Mosul attacked with car bombs in August 2004.
ISI suffered major personnel losses in April 2010, which led to Abu Bakr Al-Baghdadi (Ibrahim Al-Badri) taking over in May 2010. The new leader had an even more extensive Salafi pedigree than his predecessor, with an extended family with deep regional Salafi ties extending into Saudi Arabia's own Salafi religious elite.
On October 31, 2010, the Islamic State of Iraq launched its bloodiest, highest-profile attack on a Christian target to date, killing at least 50 worshippers during a Mass at the Syrian Catholic Cathedral of Sayyidat Al-Nejat (Our Lady of Salvation) in Baghdad. According to eyewitnesses, the gunmen made at least four claims for the killings, two general and two specific: all of the Christians were infidels; it is permitted to kill them; the killing was in retaliation for the burning of a Koran by an American pastor, and was also in retaliation for the alleged imprisonment of two supposed Muslim women converts in Egypt.
The ISI statement issued a few days later by the Ansar Al-Mujahideen forum, in the name of ISI's Al-Furqan Media Foundation, tied the attack, which may have been intended initially to be a hostage taking, not to the U.S. military presence in Iraq, nor even to the Koran burning – but to an Islamist-generated controversy involving two Coptic women in Egypt, Kamilia Shahada and Wafaa Constantine. ISI promised death to Christians in Iraq, Egypt, and Syria and throughout the region in return for this perceived wrong. Why Iraqi Uniate Catholics should deserve death for the actions of Egyptian Coptic Orthodox – actions which did not result in death of anyone – is never explained.
In the Egyptian Islamist narrative, these two were women who left Christianity for Islam, and who were then forcibly handed back to the Coptic Orthodox Church and their Christian husbands. The fact that both women eventually made public statements noting that they had never converted to Islam and that they wished to remain Christians seemed immaterial to an Egyptian and regional Islamist blogosphere that bitterly thought otherwise. The narrative feeds into a long-standing rich vein of anti-Coptic hysteria among Islamists, often involving women and sex, that has frequently led to violence in Egypt. With advances in media outreach, such hatred has gone viral.
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http://www.memri.org/report/en/0/0/0/0/0/0/8721.htm