Anti-government protesters hold a large Egyptian flag in Tahrir Square in Cairo Feb.11, 2011.

Located next to a trash dump on the outskirts of Cairo, the Salam Center is a bit of an oasis in an otherwise poor neighborhood. Dust and dirt abound, as the roads are not paved, and the city’s trash collectors, most of whom are Christians, carry huge bags of refuse on donkey-drawn carts. Children run everywhere amid the mess. The scene looks like something from another age, but it is very much 21st-century Egypt.

Inside the Salam Center, it is an impoverished, yet peaceful setting. Some 19 religious sisters, wearing habits, cater to Christians and Muslims alike. Consisting of a hospital, school and home for senior citizens, the facility is run by the Daughters of St. Mary, an order of Coptic Orthodox nuns.

Sister Maria, the head of the convent associated with the Salam Center, acknowledged that recent developments in Muslim-Christian relations have frightened her. “Things all looked good during the revolution, but now you’re seeing a lot of attacks on Christians,” she said. “It’s a bit worrisome.”

Many people in the region share Sister Maria’s viewpoint. As the Arab Spring swept through North Africa more than a year ago, it brought newfound hope for freedom. In downtown Cairo’s Tahrir Square, Egyptian Muslims and Christians celebrated the downfall of President Hosni Mubarak, who had been in power for more than 30 years. But for Christians in Egypt, who make up about 10 percent of country’s 82 million people, the elation didn’t last long.

“I thought that after the revolution we would get all our rights back, but that wasn’t true,” said Michael Eid, a 28-year-old pharmacist sitting in a church courtyard in a bustling part of downtown Cairo. “Christians are still considered second-class citizens in Egypt.”

NEW GOVERNMENT, NEW CHALLENGES

Egypt has the largest Christian population of any Arab country, but Christians remain a minority in the largely Muslim country. Most Christians in Egypt are members of the Coptic Orthodox Church, which is distinct from the Catholic Coptic Church. The latter, which is in communion with Rome under Patriarch Antonios Naguib of Alexandria, is relatively small, but still counts more than 200,000 faithful.

Although churches may be seen in many places around Cairo, there is almost always the minaret of a mosque either in front of the church or around the corner, a not-so-subtle reminder of the primary religion. If a woman in Egypt does not wear a headscarf, a tradition that has grown in recent years, it is sign that she is probably either a Christian or a moderate Muslim — in either case, a minority.

Christianity’s presence in Egypt dates back to St. Mark the Apostle, who is believed to have brought the Gospel to Alexandria, a port city on the Mediterranean, in the 1st century. St. Mark was martyred by being dragged through the streets of Alexandria by a horse, and Egypt claims a long list of saints and martyrs who lived in the centuries that followed.

“Egyptian Christians have history in mind, and it’s a history full of hardship, suffering and even bloodshed,” said Bishop Mouneer H. Anis, the Anglican bishop of Cairo. “Without the blood of the early Christians, we would not be Christians today.”

But Christian suffering in Egypt is not just the stuff of history. Christians have been killed in recent clashes as well. More than two-dozen people died last year during a demonstration at Maspero, in downtown Cairo, many of them run over by army trucks. At the funeral of the Maspero victims, Bishop Anis saw people mourn as each coffin was brought out of the church. The people, though, also applauded. “You don’t clap except for a hero,” he said.

Under Mubarak, there were some serious incidents, including instances of Christians being thrown in prison or even killed for religious reasons. But according to Bishop Anis, life for Christians is getting a bit more difficult now, with more churches burned and demolished. “That never happened under Mubarak — although it was not easy under Mubarak,” he said.

Today, the Muslim Brotherhood, an Islamic political group, controls almost 45 percent of the seats in Parliament, and the more radical Salafists control 25 percent, together giving them an absolute majority. The rest of Parliament consists of moderate Muslims and their Christian allies.

What does this mean for Christians? The answer is not yet clear, although they hope the Muslim Brotherhood will allow for some protection of minorities when a new constitution is written. Bishop Anis suggested that the Muslim Brotherhood would gain recognition from the international community if it were to protect minorities and emphasize high standards of education for young people.

Poor education is one of the biggest problems in Egypt, and can play a role in fostering religious conflict, as people are not taught to respect others who might practice a different religion or hold different beliefs. About 30 percent of the population can neither read nor write.

“This is the greatest sin of Hosni Mubarak,” said Father Antoine Rafic Greiche, a spokesman for the Catholic Church in Egypt. “He kept the people illiterate for 30 years.”

SEEKING JUSTICE

On the surface, relations between Muslims and Christians may look promising in Egypt. There is, for example, a flourishing girls school for people of all faiths that is run by Catholic religious sisters in the Heliopolis section of Cairo.

But according to Father Greiche, who lives near the school, one of the sisters was attacked not long ago by two men on a motorcycle. The assailants pulled off the sister’s habit and demanded that she say, “Muhammed is the Prophet.” They then cut her face with a razor.

“As a priest, I should not be scared, but we are a little scared,” Father Greiche said.

With the Muslim Brotherhood and the Salafists in power, Egyptian Muslims could be pushed in a much more radical direction, he added. “They will change the mentality of the society, and that’s the most dangerous of thing. It’s a very foggy night right now for us.”

Catholic Coptic Bishop Antonios Aziz Mina of Giza recalled that the uprising in Egypt initially made him optimistic about the future of the country, but that has changed. The goal of creating a modern state remains far away, he said, adding that whenever a church gets burned or destroyed, the culprit is never found.

“We’re ready to pay for the church to be repaired, but we want the guilty parties found and tried,” Bishop Mina said.

“Humanly speaking, we don’t have a great future,” he said. “But there have been worse times for Christians in Egypt, and Christians are still here. This could be a moment of purification.”

He also referred to an incident in which six Christian families were forced out of a village after reports of an illicit relationship between a Christian man and a young Muslim woman.

“Where is the law?” the bishop asked. “If today they kick us out of a village, eventually they will kick us out of the country.”

The Christian population in Egypt may be small, but it is determined. People don’t try to hide their faith; in fact, many men and women have crosses tattooed on their wrists. Their future, however, is dependent on relations with Muslims, relations that have been strained even since the Arab Spring.

Adel Abd El Malek Ghali, a medical doctor who helps out at the Salam Center, cited the lack of justice for victims of religious violence. “The truth is that if a Muslim kills a Christian, nothing ever happens,” he said.

Ghali stressed, however, that despite everything, Christians should be calm. “It doesn’t mean there won’t be persecution, but we shouldn’t be afraid.”

A man of faith, Ghali maintains a joyful disposition and has a special devotion Mary under her title Our Lady of Zeitoun, named for a miraculous apparition in a southern district of Cairo.

For Ghali and other Christians, there is still hope that the Arab Spring in Egypt will lead to a spring time for both Muslims and Christians, allowing them to live in a modern state in peace and mutual respect. But there is no guarantee that will happen, and some expectation that it may not.

Bishop Anis put it this way: “As an Egyptian Christian, I feel that hardship and suffering are part of the package. If you are a Christian, there will be a price to pay.”

GREG BURKE is the Rome correspondent for Fox News.