Mariz Tadros writes for the Middle East Institute on the campaign waged by the MB and other Islamists to blame Copts for the fall of the Morsi administration:
A few days before the protests and throughout the week of demonstrations, media sympathetic to the Brotherhood launched a campaign that represented the protests as a Christian conspiracy against Islam. The campaign was staged with an intensity that was sufficient to catalyze bloody sectarian clashes. On the Muslim Brotherhood-affiliated television channel Misr 25, Noureddin, a program presenter, made a fictitious announcement that Christians were attacking mosques. On an Islamist-affiliated channel, program guest Shaykh Mahmoud Shaaban, a Salafist, concocted a story that Christians had congregated in Tahrir Square and that their main chant was “Jesus is the solution,” as if Christians were countering the Muslim Brotherhood slogan, “Islam is the solution.”
There's a lot more there, and in my experience many Brothers have seen the protests, coup and overall crisis in sectarian terms – even if they did not want to encourage sectarian violence they saw themselves as the victims of a sectarian conspiracy in which the Church and "organized Christendom", for lack of a better word, played an important role. While it's undoubtedly true that the vast majority of Egyptian Christians were anti-MB (after all, Morsi had done little to win them over) this is a convenient recasting of the widespread anger at Morsi and the MB (to include even Islamists, never mind many ordinary Muslims) to energize a base for whom sectarianism has long been a driving motive. This is especially the case in parts of Egypt with large Christian populations, such as Upper Egypt, and it's not surprising that this is where there has been much of the sectarian violence of the recent weeks.
I also paste below an analysis from the excellent newsletter of the Arab-West Report, a inter-religious dialogue NGO and think tank. (Their website has been the victim of an attack, so it's mostly down for now.)
A statement made by al-Qa’ida leader, Ayman al-Zawahiri (Ayman al-Zawāhirī), is believed to be one of the major catalysts for ongoing sectarian clashes between Muslims and Christians and attacks by militants on the Sinai Peninsula and in other areas of Upper Egypt, south of Cairo. His fiery speech accused Egyptian Christians of seeking a Coptic state in southern Egypt and alleges that they along with “crusaders, secularists, the Americanised military, remnants of Mubarak’s regime and some affiliates of Islamic groups” are responsible for former president Muhammad Morsi’s (Mursī) overthrow and were supported by Gulf money (link).
Violence in Beni Suef, Suhag, Fayum, and other areas of Egypt have led to the deaths of Christians and some Muslims. Churches have also been attacked and vandalized in many of these areas under a variety of circumstances. In Suhag it is believed that an al-Qa’ida flag was raised on Saint George Church. Also, one of the Armenian churches in Egypt was tagged with the words “Egypt is Islamist”. Some attacks have been based on rumors of Christian attacks on Muslims, for example, while in other instances violence has been in protest of Morsi’s removal.
Egypt’s army said on Wednesday that they have the captured or killed 227 individuals on the Sinai from 5 July to 4 August —103 of who were arrested and 124 of who were either killed or injured (link). Attacks continue in the northern region of the Sinai Peninsula, most frequently in al-Arish, where several checkpoints have come under fire from militants. Other attacks in the region have included the murder of a Coptic priest in al-Arish and the beheading of a Coptic citizen in Shaykh Zuwwaīd early in July (link).
On August 7, the Prosecutor General ordered the arrest of 11 persons on charges of “murder, attempted murder, arson and possession of unlicensed weapons” following violence on Saturday, August 3, in Minya, a governorate located roughly 250km south of Cairo. The clashes are the latest in a series of attacks on Christians in Upper Egypt, which left one dead and over a dozen injured (link). Last month an attack on a Coptic church in Minya left the premises in a shambles and Father Ayoub Youssef believes that he barely escaped with his life from the attackers (link).