Children's Bibles lie in a charred pile at the entrance, while inside, exploded glass, wood and tiles crunch underfoot.

The church, which for more than a century has provided a place of worship and sanctuary for its parishioners, smouldered for days after an angry mob of hundreds of Islamists threw Molotov cocktails into the grounds and forced their way through the large, black metal gates.

Once inside, says witness Kerdos Gerghis, the mob ransacked the church, stealing whatever they could before starting the fire that destroyed the interior, leaving officials and parishioners fearful of what will come next.

The 19-year-old, who has attended this Coptic Orthodox church in the city of Minya, Upper Egypt, since he was a boy, made several frantic phone calls for help, but it was at least an hour before police arrived.

When they did, the mob, made up of a handful of locals as well as Muslim Brotherhood supporters from the outlying villages, turned on them and a gunfight broke out between the Islamists and the police.

“The relationship between Christians and Muslims in this community is usually very normal, and so many Muslims have stepped in to help us defend the churches,” he says. “I have watched Muslim families cry as they see our churches burn.”

But with courage comes punishment. A young Muslim man who helped his Christian neighbours try to extinguish the blaze was killed the next day in an act of retribution, Gerghis says.

It is a story repeated time and again throughout Egypt. As the political crisis deepens and the sectarian violence cleaves further into communities, Christians have increasingly been targeted by Muslim Brotherhood supporters intent on revenge.

At least 32 churches and monasteries as well as countless schools, homes and businesses in nine cities around Egypt have been targeted by Islamists on a rampage following the downfall of their president, Mohamed Mursi, Human Rights Watch has found.

It is not difficult to find burnt-out buildings in Minya, where an estimated 35-40 per cent of the population is Christian. In one street, the remains of an old building that housed a clothing shop owned by a Christian family is still smouldering; in another, a large Christian orphanage has been destroyed.

We pass firebombed cars, while the nearby Good Shepherd School and convent next to it have been destroyed by fire.

Most of the attacks occurred on Wednesday, as the Egyptian Army and riot police were carrying out their operation to clear the Muslim Brotherhood protest camps at the Rabaa Al-Adawiya Mosque in Nasr City and al-Nahda Square in Giza.

Egypt's Ministry of Interior puts the nationwide death toll from the August 14 violence at 638 people, including 43 police officers, with more than 4200 injured. Other estimates put the death toll at between 800 and 1000 people.

Attacks on churches and Christians surged after Mursi's ouster on July 3, in provinces as far afield as Luxor, Minya, Beni Suef, Sohag and Port Said.

In Sinai, a Coptic Orthodox priest was shot dead, while a Christian shopkeeper was kidnapped and found beheaded, local media reported.

Four hours from Cairo, in Upper Egypt, the attacks have been steadily worsening over the past week, says Bishop General of Minya Anba Macarius, who is critical of the feeble response from the army and police.

Their lack of action to protect churches and other Christian buildings has created the perfect environment in which “crime and terrorism flourish”, Macarius tells Fairfax Media from the offices of the Minya diocese.

Local imams have tried to make contact, he confirms, but the church is not yet ready to speak.

“First we must protect the Christians and the feelings of those who have suffered loss,” he says. “Now we are calling on the state to protect the churches and the army to come onto the streets.”

It is with a heavy heart that caretaker Ashraf Makram unlocks the doors to the Good Shepherd School, his home for 45 years. His living quarters have been totally destroyed and the courtyard is filled with the remains of burnt furniture and destroyed cars.

“We called and called for the police to help but they would not come,” he says. “I have never seen anything like this in all my time here – the neighbours all gathered, both Muslim and Christian, to try to contain the blaze but we could not.”

As we are talking, Domadios Samir, who teaches computer sciences, arrives at the school.

Along with other locals, he confronted the gang of hundreds of Brotherhood supporters who were first looting and then burning the buildings and cars.

Samir asked them why they were attacking the school. “This is a school for the unbelievers,” they answered.

An impossible choice

“We had a choice between cancer and death,” says Father Youhanna Makin of the proverbial Catch-22 situation in which Egyptians found themselves in June last year, when choosing the country's first democratically elected president.

The presidential run-off was between Ahmed Shafiq, a former senior commander in the air force who served as the last prime minister of Hosni Mubarak's government (cancer) and Mursi, the Muslim Brotherhood's candidate who narrowly won with 52 per cent of the vote (death).

“The Copts chose cancer but we got death,” Makin says wryly from his office in the St John The Baptist Church in downtown Cairo. “And now there's been a resurrection [the June 30 revolution].”

But, he says, Copts remain incredibly vulnerable to the anger of the masses.

Egypt's Christians are believed to make up about 10 per cent of the country's 85 million people and they have watched with growing concern the rise of both political Islam and militant Islamists since Mubarak was forced from government in February 2011.

Despite the challenges, Makin says, “we are encouraging Copts to step outside and into political life, whatever their views.”

“A lot of people who had not been out onto the street came out and demonstrated on June 30,” he says, of the huge rally that called for the downfall of the Mursi presidency and led to the military's intervention on July 3.

But in Upper Egypt, where many of the attacks on Christians have occurred, a combination of poverty and poor education, mixed with the current political turmoil, has created a volatile situation, he says.

Much of the lawlessness comes from the idea, pushed by the Muslim Brotherhood during Mursi's year in office, that religion must be the ultimate arbiter of a society.

“What we need is a country run by law, not by an interpretation of religion by a small group of people,” Makin says. “For this to happen, we need a whole new constitution, not a rebuilding of the Muslim Brotherhood constitution Mursi forced through in the middle of the night that bypassed any verdict of the court.”

An easy target

It is not easy to criticise an enemy as powerful as the Egyptian military, says Adel Iskander, a fellow at the centre for contemporary Arab studies at Georgetown University in Washington.

“So from the Islamist standpoint, when you blame the military and in particular General Abdel Fateh al-Sisi for the overthrow of Mursi and everything else that has ensued ... the Copts are an easy adversary when the military is too powerful to confront.”

Also, Iskander says, Copts are relatively unprotected in Egypt.

“It is both a blessing and a curse – they live in every province and governorate, every community has Copts, they are in every area and they are part of a wide cross-section of Egyptian society but this means it is often very difficult to protect them from this kind of violence.”

Add to that, Christians have literally been written out of the public school curriculum, effectively extricating them from modern Egyptian identity and rendering their religion an unknown quantity for many Muslims, he says.

“Most Muslims know Copts who are their neighbours or their co-workers but they know very little about their religion, their rituals,” says Iskander, who has written a just-released book, Egypt in Flux: Essays on an Unfinished Revolution.

Mubarak convinced the Coptic community that the only way to exist safely in Egypt was have the protection of “secular” state, and “with that came authoritarianism”.

Deepening the isolation of many Coptic Egyptians was the stance of the former Pope Shenouda, who died in March last year, he says.

The pope monopolised every aspect of Coptic life, from politics to social services and leisure activities, corralling many believers within the strict confines of the church.

The end result, he says, is that Copts are “drastically and remarkably under-represented in political life and in almost every public vocation – arts, music, sports – they are practically invisible.”

A critical juncture in the political awakening of the Coptic community came in October 2011 with the incident that is now known as the Maspero Massacre.

Twenty-five people died and more than 320 were injured when a Coptic protest against the failure of the government to investigate an attack on a church was overrun.

Egyptian soldiers drove armoured personnel carriers into the crowds of protesters, dragging some under the wheels in scenes of terrible carnage.

To many it was the first time the military, traditionally seen as the protector of the Coptic community, had deserted them.

“It put the church in a very awkward position where they either had to come out and condemn the most powerful institution in Egypt – the military – or sit in silence,” Iskander says.

“The anger of the community could not be contained ... the Coptic masses were moving and the church was barely keeping up.”

The new leader, Pope Tawadros, is younger and more perceptive than his predecessor, Iskander says, in a comment echoed by many interviewed by Fairfax Media for this article.

Even though Pope Tawadros, along with Sheikh Ahmed el-Tayeb, the Grand Imam of Al Azhar, the most important Islamic institution in Egypt, publicly supported Sisi in his removal of Mursi from the presidency, he has in general taken a step back politically, he says.

“Practically every institution has had a head-on collision with the Brotherhood,” says Iskander, and in this case, Christians have paid dearly.

For author and satirist Moheb Samir, the idea that everything in Egypt is seen through the prism of religion is part of the problem.

“A fight between a Muslim and a Christian who are both selling vegetables becomes a fight between a Muslim and a Christian, instead of a fight between vegetable sellers,” says the 32-year-old over a cappuccino in a cafe overlooking the Nile in the middle-class Cairo suburb of Zamalek.

It is a long way from his family home of Mallawi, south of Minya, where he says relations between the religions began to fracture years ago, and have only worsened in the past two years.

Samir uses humour to write about the differences between religions, in the hope that by gently dispelling myths about Muslims (that they wear no underwear under their robes or abayas) and Christians (that in one month of scandalous “fun” everybody kisses everybody), the two can live more harmoniously.

“When you actually examine the rumours, you realise that we really do not know each other very well at all,” Samir says.

Ultimately, Copts cannot “just live inside the walls of the church”.

To rebuild a new Egypt, he says, people must work on the relationship between the two faiths until it reaches “a good place where everyone feels that they can claim their rights as Egyptian citizens”.