Robert Fisk: Violence shows uneasy place of minorities after Arab Spring

The statistics are easy, the future is not. Up to 20 million Copts in Egypt, 10 per cent of the population, the largest Christian community in the region. But President Anwar Sadat once described himself as "a Muslim president for a Muslim people" and the Christians have not forgotten it.

Sure, the attack on the church in Aswan helped to stoke the fires, and the 26 dead are the largest number of Egyptian fatalities since the two worst days of the revolution which overthrew Sadat's successor Hosni Mubarak. But Christian fears – stirred by "Amu Hosni" himself when he thought the throne was slipping from under him – meant the leadership of the Coptic church did not support the revolution until two days before Mubarak's fall.

The Copts are Egypt's original Christians. They were the majority during Rome's rule in antiquity, when the Prophet Mohamed had not been born. But are the Copts Arabs? Some Christians say they are. Some say they are the "original" Egyptians – a bit much when the Muslims now outnumber them 10 to one. During the revolution, they arrived in Tahrir Square on Sundays to pray – protected by Muslims. When Muslims prayed in the square on Fridays, some Christians came to help protect them. But that was then.

There will be the usual Cairo conspiracy theories about the terrible deeds of Sunday night. But there lies behind all this a far more profound problem. Christians in many Middle East nations have always been told that they are minorities, and must rely on their governments to protect them. The assassinated Lebanese Prime Minister used to tell Christians that "Patriarch Sfeir is my friend" – not as close, perhaps, as Hariri thought. Now the new Lebanese Maronite Patriarch, Bechara Rai, has come in for a lot of flak for suggesting in Paris that the Syrian regime should be "given a chance" to resolve the country's problems, a remark he claims is a falsification of his words, but which earned him the apparent withdrawal of an invitation to meet President Obama.

Jordan hosts Christian communities; there is even a tiny community of French Christians in Algeria. In 1996, seven French monks were taken from their monastery at Tibhirine and killed – possibly in a screwed-up military ambush of their Muslim kidnappers – and the Archbishop of Algiers told me he had to identify their severed heads hanging from a tree. "You cannot help remembering that Jesus was murdered by human violence," he said – "and in the name of religion."

There's nothing new about "religious" violence in Egypt. But, of course, Egypt's revolution was supposed to be cleaner than this, a shining path to a new future which all Arabs will want to emulate. Well, perhaps. The journalist Abdel Bari Atwan has often said that "these things" – revolutions – "are not perfect". He'll be saying it again today, no doubt. It is a sorrowful business, reflecting the anger of Christians as well as Muslims, and the long path that revolutions must travel to bring freedom to the people of Egypt.