WASHINGTON — An Islamist president, Mohammed Morsi, will take office in Egypt. The landmark event June 30 could fulfill the hopes of protesters in the region who have taken part in the “Arab Spring” uprisings — or spell doom for dwindling religious minorities, mainly Christians, who face an uncertain future.

The Obama administration acknowledged the dangers ahead when it greeted the election of Morsi, a member of the Muslim Brotherhood, with cautious optimism, signaling that the new Egyptian leader will have to earn Washington’s endorsement.

U.S. Secretary of State Hillary Clinton welcomed Morsi’s pledge to respect Egypt’s treaties with other nations and praised the powerful Egyptian military for “facilitating” the election.

“We expect the transition to continue as has been promised by the [military], and we expect President-elect Morsi, as he forms a government, to demonstrate a commitment to inclusivity that is manifest by representatives of the women of Egypt, of the Coptic Christian community, of the secular non-religious community and, of course, young people,” said Clinton, clearly leveraging Washington’s dominant role as a major source of foreign aid for Egypt.

Clinton’s statement was a good first step, but many religious-freedom activists continue to question whether this administration — or any future administration — will adopt a strong, active role in advocating for religious pluralism in a region where religious minorities are often treated as second-class citizens and where the flight of ancient Christian communities has virtually erased their presence in parts of the region.

During a meeting this week with religious-freedom activists and representatives of embattled religious minorities from Egypt, Iraq, South Asia and Nigeria, Cardinal Christoph Schönborn of Vienna, Austria, faced the problem head-on. He noted the virtual extinction of Christianity in northern Africa and elsewhere and challenged complacency about its survival in Egypt, Syria and Iraq.

“If you want to export democracy — I address our American friends — in these countries of the Middle and Near East, then help the Christians and other minorities to breathe,” stated Cardinal Schönborn. “Help the Copts to be free, help [religious minorities] in Syria to maintain … the space of freedom.”

Over the past decade, Cardinal Schönborn has watched the flight of Iraqi Christians from their ancestral villages with great concern, sharing information about their plight with Catholic bishops’ conferences in Europe. The Church leader from Austria leader has also dialogued with Muslim groups about ways Christianity and Islam might peacefully coexist.

Last year, he asked the Washington-based Center for Religious Freedom at the Hudson Institute to organize a conference that could provide a forum to discuss the problems of the region’s religious minorities and strategize about influencing the direction of U.S. policy, which often discounts religion’s role in geopolitics.

The conference, "Persecuted Christians and Other Religious Minorities in the New Middle East: Formulating an Effective U.S. Policy Response," took place just days after an Islamist won Egypt’s presidential election and news organizations in Syria reported fresh violence amid the nation’s civil war.

In Egypt, Bishop Kyrillos William issued an open letter June 27 to Morsi on behalf of the Coptic Catholic Patriarchate of Alexandria, expressing his community’s hope that the new president would create an inclusive government. There are 250,000 Catholic Copts among an estimated 8 million to 10 million Christians in Egypt — the vast majority being Orthodox.

“We are confident that, with the help of the Almighty, and with your wisdom, you will be able to work for the best interests of the nation and its people,” wrote Bishop William, putting the best face on a situation that has already prompted many Copts to initiate plans for their departure.

At the Washington conference, Cardinal Schönborn acknowledged that the rise of Islamist political movements was sowing fear among Christians, who had helped to establish secular government in the region during the 1950s that saw the rise of Arab nationalism.

“The Christians and other minorities in the Near East know their only chance of survival is the secular state with real religious freedom,” he said, noting that Christians “stand firmly against any form of theocracy.”

He reminded conference participants that the United States has played a critical role in the region and asserted that the U.S. government’s military intervention and diplomatic failures in Iraq had contributed to the flood of Christian refugees.

Since the 2003 U.S. invasion, Iraq’s ancient community has been cut in half, as many fled the violence and disorder that followed the end of Saddam Hussein’s regime and the U.S. military’s failure to secure a stable transition in the months that followed.

The U.S. government, said Cardinal Schönborn, “must not repeat in Syria and elsewhere the mistakes of Iraq. It is a fact there were serious mistakes in Iraq. … Syria and Egypt must not become Iraq.”

Further, Cardinal Schönborn stressed the importance of Western nations developing a more complete understanding of cultures in a region undergoing political transformation, including the role of religion.

Richard Land, the president of the Southern Baptist Convention’s Ethics & Religious Liberty Commission since 1988 and a speaker at the Washington conference, noted that U.S. diplomats frequently ignore religious issues, reflecting the secular training that has shaped many American policymakers.

Quoting former U.S. Secretary of State Madeleine Albright, Land suggested that the U.S.  diplomatic corps “missed the Iranian revolution because they discounted the mullahs.”

During an interview, Land observed that the same mistakes are being repeated right now.

“The Arab Spring didn’t turn out the way the State Department thought it would because they discounted the role of religion and the Muslim Brotherhood.”

Nina Shea, the director of the Center for Religious Freedom at the Hudson Institute, noted that other religious minorities have also felt the impact of political instability.

“All but a handful of Jews have been driven out of Iraq and Egypt,” she told the assembled activists, who were focused on events in Egypt, Iraq, Syria and Lebanon.

“Christians comprise the largest non-Muslim majority in the region,” she added, and the political turbulence is “affecting old and new churches. … Some call it ‘the ecumenism of the martyrs.’ Because their presence in the region is at risk, religious pluralism itself is at risk.”

Habib Malik, an associate professor of history and cultural studies at the Lebanese American University, another speaker, decried the practice of “armchair experimentation” among those policymakers in the West who have encouraged change in the region without pressing for assurances that religious minorities will be protected. “No one wants to be the guinea pig for this kind of experiment,” said Malik.

He called for Western governments and aid donors to “proactively put potential violators on notice that they will be watched like a hawk — not just regimes, but replacements must also be put on notice.”

Like many U.S. activists on the issue, Shea wants the State Department to strengthen the implementation of the International Religious Freedom Act, passed in 1998, which has encouraged a new generation of American diplomats to give more priority to the promotion of religious pluralism abroad.

The International Religious Freedom Act calls for an ambassador-at-large for international religious freedom, an advisor on the issue in the National Security Council, and a bipartisan U.S. Commission on International Religious Freedom.

At the conference, Cardinal Schönborn briefly turned his attention from the ancient religious communities struggling for survival to the rights of newly arrived Christians from India, Sri Lanka and the Philippines in Saudi Arabia, where there is no religious freedom.

“One million Catholics are living in Saudi Arabia, as servants, housemaids, with no religious rights at all.” He noted that Washington “has enormous influence in Saudi Arabia. The question of religious freedom for these large minorities should not be forgotten.”

Generally, European and U.S. bishops only speak out on international religious-freedom issues and related concerns after consulting with local churches in the region.

Earlier this month at the U.S. bishops’ meeting in Atlanta, Iraqi Chaldean Auxiliary Bishop Shlemon Warduni of Baghdad urged American Catholic leaders to press the White House to defend his beleaguered community. Bishop Warduni spoke out about the importance of advancing religious freedom in U.S. domestic and foreign policy, defending not only the right to worship, but also the freedom to witness to faith in the public square.

In recent months, Syria has been the latest country in the region to experience increased political violence.

In April, Bishop Richard Pates of Des Moines, Iowa, the chairman of the U.S. Catholic Conference of Catholic Bishops’ Committee on International Justice and Peace, wrote to Thomas Donilon, President Obama’s national security advisor, to express concern about the mounting refugee problem in Syria. The letter called attention to an estimated 50,000 Christians who “have left Homs, traditionally home to one of the largest Christian communities in Syria.”

“The U.S. bishops are in solidarity with Pope Benedict’s call for a peaceful resolution to the conflict in Syria,” read the letter, which called for ongoing humanitarian aid to refugees and asked the U.S. government to continue to work through multilateral channels, to restore stability in the region, while protecting the human rights of all people, including Christians.

Stephen Colecchi, the director of the USCCB’s Office of International Justice and Peace, confirmed that the bishops recently made “pastoral visits” to Iraq and Egypt. At the end of July, there will be a visit to Nigeria, where Christians have experienced a rise in violent religious persecution.

“We go to places to learn from the local Church and find out what would be helpful in their struggle,” said Colecchi, who noted that some advocacy remains low-key in order to avoid reprisals for local Churches.

That said, he observed that embattled Christians don’t allow real concerns about survival to undermine a profound sense of hope.

“The Church always lives in hope,” he said, recalling that when he met with Egyptian Christians in January he “was amazed by their hope.”

Joan Frawley Desmond is the Register’s senior editor.