Just as Pope Francis was holding a mass for 25,000 Coptic Christians in a Cairo stadium this weekend, around 30 Muslim schoolgirls arrived at the Coptic Museum in the old centre of the capital. They took photographs of each other and selfies against the facade of the museum. For the front wall of this magnificent building was constructed by Marcus Simaika Pasha in 1910 to resemble the facade of a mosque. This was a quite deliberate decision by Simaika: his idea was to illustrate in stone how intertwined are Egypt’s Christians and Muslims, not only in religion but in culture.

But that was then. It was, of course, the Pope’s message this weekend, along with that of the Sheikh of al-Azhar, Ahmed al-Tayeb. Their message of peace was broadcast around the world. Their far more striking remarks – in almost identical words – about the evils of arms manufacturers who sell their products to the Middle East, was predictably ignored. Journalists understandably went for the most obvious story: both Muslim and Christian leaders condemned (no name mentioned, of course) the Isis ‘Caliphate’ – which Pope Francis excoriated in the memorable phrase “the incendiary logic of evil” – and the attacks on Christian churches by the Egyptian variety of the Isis cult. Yet the problems of Egypt’s Christians go rather deeper than this.

I went to see an old Egyptian friend, a Muslim called Ahmed – his real name, although it tells you a lot about the Egyptian regime that he insisted I did not identify his family name – who lives near the Coptic quarter of Cairo, fringed by the rail tracks to Helwan and the remains of one of the great Roman gateways to the ‘Babylos’ city of ancient Cairo, built by the Emperor Trajan. And this is what he said about his neighbours: “I tell you I have many Christian friends. They are real friends and very dear to me. They are my brothers. But the problem is that many Muslims see how close they are to the government – the government of President al-Sisi – and they blame the Christians for anything that goes wrong. Today, whenever a dispute arises between a Muslim and a Christian – about property, a shop, prices, any argument – it becomes a Muslim-Christian argument.” In other words, it becomes a sectarian argument.

37 killed in Islamic State bomb attacks on Egyptian churches

Dethroned president Mubarak always emphasised his affection for the Christians. His assassinated predecessor, Anwar Sadat feuded with the Coptic church, imprisoning its Pope and sensationally and foolishly claiming that he was “a Muslim president for a Muslim people” – which didn’t greatly please the Christians. Mubarak actually encouraged the impressive restoration of the Coptic museum. Then when Sisi staged his coup against the elected president Mohamed Morsi, there was the Coptic pope in one of the first post-coup photographs, standing next to Sisi.

It’s not difficult to spot the problem here. As a minority (maybe 10 per cent of Egyptians), Christians naturally need the regime to protect them. Their fear – that the government deliberately failed to guard their churches (untrue) and the ignorant attacks on them by equally untrained, untaught Muslim preachers in upper Egypt (sadly true) – drew them closer and closer to Sisi. They became associated with the regime itself.

Christian minorities have suffered in the same way all over the Arab world. Christians in Syria largely support the Assad government because it tries to protect them. The most recent footage of Bashar al-Assad shows him visiting a Christian monastery north of Damascus. When the Maronite patriarch of Lebanon, conscious of his fellow Christians in Syria, failed to condemn the Assad regime, Barack Obama – in one of his ‘holy’ moments – refused to see him in Washington. Christians in Iraq always felt they had special protection from Saddam; and within months of Saddam’s overthrow at the hands of the Americans, they were fleeing for their lives.

Another longstanding friend (again, a Muslim but this time unwilling even for his first name to be revealed) agreed with Ahmed but thought the “foreign media” had done much to embitter relations between Muslims and Christians. “They like simple stories,” he said. “That means persecuted Christians. It also means that even the police who are here to protect Christians are frightened of journalists.” More frightened of reporters, I dare say, than they are of Isis. With good reasons? But my friend also saw another pattern in the life of Egypt. “It has turned into a Muslim Brotherhood army fairground,” he said. “It’s like Turkey: you get Islamists in charge and then the army ‘returns’ to save the people. It happened here. And it will happen when Turkey decides to get rid of Erdogan – the army will return.”

The Egyptian philosopher Farag Fouda, murdered by Islamists in 1992, had a similar point of view. He predicted at the 1992 Cairo book fair that there could be a “horrifying cycle” in which “the military rule will lead to a (Muslim) religious one and (this) will not be removed except by a military coup which in turn will hand power to another form of religious ruling, and so forth.” Egyptian journalist Sara Abou Bakr wrote only four years ago that Fouda had anticipated what was then happening in Egypt: the Muslim Brotherhood under Mohamed Morsi came to power after the military’s undeclared candidate lost the election and might soon lead to a coup. It did.

Fouda’s death – this is just to reinforce the ignorance of the Muslim killers – almost certainly came about because he had condemned the “religious state” and challenged his book fair audience to name a single democratic religious state. During the trial of one of Fouda’s killers, one of them was asked why he committed the crime. Because of his books, he said. Asked which particular book had upset him, the youth replied: “I don’t know how to read.” Morsi was later to pardon one of Fouda’s killers.

All this was a subtext to the Pope’s long speech this weekend at the ‘International Peace Conference’ in Cairo which he shared with Sheikh al-Tayeb. He spoke of the “incivility of conflict”, the need for religious leaders “to unmask the violence that masquerades as purported sanctity”. Vatican speech writers, who used to be poor on history but good on politics, are now good on politics – though less good on history if the former Pope Benedict’s ridiculous performance at Regensburg was anything to go by – surely got it right, however, when they had Pope Francis condemn the arms trade, the “murky manoeuvrings that feed the cancer of war”. What is most instructive, however, is that the Western nations who so often condemn attacks on Egyptian Christians, had absolutely nothing to say of these remarks, nor of al-Tayeb’s comments on the enriching of individual arms manufacturers.

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Of course they did not. Because the Trumps, Mays, Merkels and other leaders of our ‘civilised’ West – not to mention our Russian friends – are the primary beneficiaries of this vile trade. We need to keep the arms flowing to the Middle East – so we do. And if we wish to play innocent, who can deny that much of Isis’ firepower has come from US weaponry captured from the Iraqi army in Mosul. I’ve seen some of it on Syria’s front lines, including newly destroyed US missiles and American M1A1 Abrams tanks.

But here we should perhaps return to the beautiful Coptic museum in Cairo. It contains remarkable Christian icons and columns, gowns and texts which clearly show Pharaonic, Roman and Islamic influence. Some bibles are written (by hand, of course) in both Arabic and ancient Coptic. Some of the texts are written on clay or stone because papyrus was too expensive for most Egyptians of the time. Of the 6,000 papyrus works, the most important are perhaps the Psalms of David, found lying in a grave beneath the head of a dead little girl. What mourning hands put this text beneath her?