JUDY WOODRUFF: Now, in the final story from her recent overseas reporting trip, Margaret Warner looks at Egypt's Christians, who have been victims of dozens of attacks since July.
MARGARET WARNER: The attackers came at night to the Church of the Virgin Mary, for more than 60 years a Coptic Christian sanctuary in the village of Kafr Hakim.
Fifi Awad worshiped there.
FIFI AWAD, Egypt (through interpreter): They attacked the church. They took everything they could take, the generator, the refrigerator, even bags they thought had donation money. Then they burned the first and second floors and said, "Allahu akbar."
MARGARET WARNER: Guard Emile Moussa was on the job, but he felt powerless.
EMILE MOUSSA, guard (through interpreter): A march came towards the church yelling, "Islamic, Islamic" and cursing the pope and Christians. I started to call the police and the military, but no one answered.
MARGARET WARNER: The timing was no coincidence. Earlier that day, August 14, hundreds of Egyptians were killed by security forces as they cleared two sit-ins protesting the military's ouster of Egypt's president, Mohammed Morsi of the Muslim Brotherhood.
Retaliation came swiftly against Christian churches and police stations around Egypt. When the smoke cleared, more than 40 churches had been damaged or destroyed. Most were in fiercely Islamist areas of southern or upper Egypt and a few in Cairo's outskirts, too. Amid the chaos that night, some Muslims like Nagah Azab came to the aid of their Christian neighbors.
NAGAH AZAB, Egypt (through interpreter): Christians are more than brothers to me. We live together and it is good for us both. I want you to know that we are the ones who protect Christians, as we did when the young men came and attacked the church on orders of the Muslim Brotherhood.
MARGARET WARNER: Yet, even now, Awad says she lives in fear.
FIFI AWAD (through interpreter): We are so afraid for our families and children. We are afraid as Christians to wear the cross.
MARGARET WARNER: Coptic Christians have worn that cross in Egypt for centuries. Tradition has it the faith was brought here by the Apostle Mark. Egypt was majority Christian until the 10th century, when Islam spread.
Even today, with an estimated 10 percent of this country's 85 million people, Egyptian Copts are a significant number. But they don't always live comfortably, says Georgetown University's John Esposito.
JOHN ESPOSITO, Georgetown University: This is an ancient church. It's the largest -- most people would say it's the largest Christian community in the Middle East. But, in the modern period, Copts have continued to experience forms of discrimination, hate crimes, attacks on Copts, and attacks on churches.
MARGARET WARNER: In that period since the 1950s, under a series of strongmen Egyptian rulers, Christian Copts were free to practice their faith, but were second-class citizens in other ways.
And during outbursts of Islamist terrorism here, like the 1990s, Christians were targeted. But since the 2011 revolution that deposed Hosni Mubarak, especially after Morsi came to power in 2012, Christians came under pressure as never before, says Mona Makram Ebeid, a Copt, former professor and one-time parliamentarian.
MONA MAKRAM EBEID, former Egyptian parliamentarian: Every month or every other week, we had a church attacked, Christians killed. Sectarian violence has increased much more in the past year than it was before.
MARGARET WARNER: Georgetown's John Esposito agrees, especially when it comes to the last two-and-a-half months since Morsi's ouster.
JOHN ESPOSITO: I think that is the nature of what's going on in Egypt right now. I think the attacks stand out as much more threatening.
MARGARET WARNER: Human rights investigators say, though some Muslim Brotherhood members were involved in last month's rampage against Christian churches, it wasn't a campaign that appeared to have been directed by the leadership. But that's not the view of much of the public, as we found in the Shubra district of Cairo, with a big Coptic population.
A local Muslim landlord, Mona Gharib, had no question who was behind it.
Do you really think it's the Brotherhood themselves or do you think it's the extreme Islamists?
MONA GHARIB, landlord (through interpreter): It was the Brotherhood, because they wanted to bring back Morsi, but he's never coming back.
MARGARET WARNER: She introduced us to a Coptic shopkeeper, who insisted there's no ill feeling between ordinary Christians and Muslims here.
MAN (through interpreter): Muslims and Christians, we are one hand. And any external attempt to divide us will never happen.
MARGARET WARNER: Who do you think is trying to divide you?
MAN (through interpreter): The Muslim Brotherhood, they are not Muslims. They are terrorists and their actions are not Islamic. Even if all the churches are burned, we will pray in the mosques. We all worship the same God.
MARGARET WARNER: And when she took us to the Church of the Virgin Mary and Archangel Michael, the pastor, Father Raphael Ramzy, struck the same theme.
Have there been any threats against this church?
FATHER RAPHAEL RAMZY, Church of the Virgin Mary and Archangel Michael (through interpreter): No, because our Muslim brethren protect us here; we are like a big family. Far away from the Muslim Brotherhood, we are a family.
MARGARET WARNER: The accusation that the Brotherhood was behind the church attacks is an insidious lie, insists Amr Darrag, a former minister in Morsi's government and a top official in the Brotherhood's political wing, the Freedom and Justice Party.
AMR DARRAG, Freedom and Justice Party: The attacks on the churches in Minya (INAUDIBLE) were done by thugs who are historically related to the security forces. And he actually called -- many times, he called the security forces to come and help in protecting the churches, but they declined.
MARGARET WARNER: So the Brotherhood was completely uninvolved in these attacks on churches?
AMR DARRAG: One hundred percent, definitely. This is an old technique that has always been used, unfortunately, by the -- some parts of the security forces to put a wedge between Muslims and Christians in the country and show the world that there is a problem.
MARGARET WARNER: So that leaves the question why? Why do Coptic Christians become targets in times of national stress? Some see political motives behind the latest attacks. Morsi had accused Christians of being among his chief opponents. And when General Abdel Fattah al-Sisi announced he'd deposed Morsi, he was flanked by civil and religious figures, including the Coptic pope.
But Mona Zulficar, a prominent corporate lawyer, a Muslim who also fights for women's and minority rights, thinks the animosity goes deeper than that, among the ranks of Islamic fundamentalists.
MONA ZULFICAR, Egyptian Constitutional Committee: There is a part of the extremist view looks at the non-Muslims as infidels, and this is not true Islam. I mean, I must underline this. This is a malicious, abusive interpretation that has no foundation in the holy Koran.
MARGARET WARNER: As a member of the committee now rewriting Egypt's Constitution, Zulficar is pressing for it to include a guarantee of equal rights and opportunities for all Egyptians.
Now, you are not a Christian. You're a Muslim. Why is protecting the rights of Christians so important to you?
MONA ZULFICAR: If you start discriminating between people, you are destroying the social fabric of the society.
MARGARET WARNER: That social fabric for Christians has been destroyed in other parts of the Middle East since the onset of the Arab spring, in Syria during the current civil war, and particularly in Iraq, where it's believed more than half of all Christians fled during the years of sectarian violence there.
So what does the future hold for Christians in Egypt?
Georgetown's John Esposito:
JOHN ESPOSITO: The question of the future is a super serious question. In the last couple of years, there's been an upsurge from North Africa or from Egypt all the way over to Malaysia and even to a certain extent in Indonesia of incidents involving anti-Christian groups.
And given the -- if you will, the still chaotic situation in Egypt, and certainly Iraq, which seems to be falling apart, the worry has to be that the situation can clearly get worse.
MARGARET WARNER: Mona Makram Ebeid concedes some younger Copts have left Egypt, but she has no intention of buckling under the pressure.
MONA MAKRAM EBEID: The Christians have been here before Islam and this region, so they are solidly ingrained in the soil of Egypt. We have a past, we have a history, and so on. So, we will fight for that.
MARGARET WARNER: And for a future that Egypt's Coptic Christians hope can be theirs, too.
JUDY WOODRUFF: You can see more of Margaret's reporting from Egypt on our World page. Next week, she will be reporting from New York at the United Nations General Assembly.