The dominant story coming out of Egypt right now continues, and with good cause, to be the growing conflict between the Islamist Muslim Brotherhood and the so-called "secular" coalition that is backing the nation's military elites, a coalition that includes many mainstream Muslims, liberal secularists, Coptic Christians and members of other religious minorities.

For the most part, this hellish conflict -- which could grow into full civil war -- is being portrayed as a fight between Islamism and secularism. However, the ongoing persecution of the ancient Coptic Christian minority, a persecution that has taken place to varying degrees over the decades and centuries, shows that the reality is more complex and confusing than a mere two-sided standoff.

I have been quite critical, at times, of The Los Angeles Times coverage in Egypt. However, it's team on the ground in Egypt has now produced a story on the recent Coptic church burnings that does a pretty good job of showing just how confusing the current realities on the ground are for religious minority groups -- the degree to which they are caught in a lesser-of-two-evils endgame. Here is a crucial slice of the report:

"The Muslim Brotherhood wants to burn down the country," said Nagy Shokrallah, a fidgety man thumbing through photos of church damage on his BlackBerry. "When we take our children to visit the monasteries in the south, we tell them they were burned twice in history: the first time under Roman occupation and the second time by the Muslim Brotherhood" as Morsi and its other leaders were pushed from power.

Two Christians have reportedly been killed in recent days. Churches, schools, convents and at least one Christian orphanage have been attacked, torched or robbed, many of them in the southern deserts. Vestments have been scorched, statues shattered. Police have often provided little protection; parishioners said security forces didn't arrive at St. George's until three hours after the gunmen had fled.

"The military and police secured nothing at all," said Tony Sabry, a member of a Coptic youth union, who criticized Gen. Abdel Fattah Sisi, commander of the armed forces, for instigating a purge against the Brotherhood that left Copts exposed. "Sisi has said he will restore the churches ... but he should have protected them before their sanctity was violated."

It's crucial to note that the Copts do not believe they can trust the police and military to protect them. Why? Because the simple truth is that the vast majority of Egyptians want some kind of Islamic state and the role of the nation's religious minorities in that future state is problematic, to say the least. At the same time, there are many Egyptian Muslims who see the ancient Copts -- to one degree or another -- as part of the nation's past and its future.

Thus, some Muslims have helped protect the churches and monasteries, while others have attacked them. That's the reality: This conflict INSIDE ISLAM can be seen throughout Egyptian life. If the military elites win, that reality will remain -- only at less urgent threat level.

More on that in a minute.

Meanwhile, what happens to the Copts? What role will American and other nations in the West play in helping protect Jews, minority Muslims, Copts and others in this very threatening drama?

The Times team notes that thousands of Copts began fleeing the nation as the Islamists began their ballot-box ascension. Where will they go? Where can they go? Someone needs to cover that story at the U.S. State Department and the U.S. Commission on International Religious Liberty. After all, there is no safer home for Christians in the Middle East. The Times story notes (including quotes from a Coptic believer named Michael Fayek):

The perception in much of the country, even among Christians, is that the U.S. has been unfairly critical of the army's crackdown, which has seen more than 900 people killed in recent days, most of them Brotherhood supporters and anti-army demonstrators slain by security forces. Many here subscribe to the military's version that Brotherhood followers are terrorists.

That suits the interests of the Saudi monarchy, which fears that populist Islamist movements such as the Brotherhood could rise up against it one day. The Saudis pledged $5 billion in aid to Cairo after Morsi was deposed. Fayek applauded the gesture even though Saudi law would call for his beheading if he showed up there praying over a Bible. Many such strange alliances have arisen in Egypt, where these days many prefer security over civil freedoms.

How long can believers in minority religious groups live like that? They have lived like that for centuries.

Finally, for reporters and others interested in the foundational realities looming over these stories, let me point, once again, to some of the research done by the Pew Research Center, care of an online newsletter called The Weekly Number. This article is called: "5 things to know about Egypt, as churches burn, a mosque is sieged & hundreds die."

Let me call specific attention to No. 3 and No. 5:

3. Sectarian violence -- as occurs in Egypt -- is strongly associated with high government restrictions

Sectarian violence in Egypt is not a new phenomenon, but it appears to be on the rise. For instance, prior to last week's violence, Al-Jazeera reported that confrontations between Muslims and Copts have increased in Egypt since the overthrow of Hosni Mubarak in 2011. And Amnesty International reported on a recent increase in tensions in Wasta (about one hundred kilometers south of Cairo), highlighting the vulnerability of Egypt’s Coptic Christians, the largest religious minority in the country.

The violence by and toward the Muslim Brotherhood, however, is also a form of communal violence within the Muslim population, pitting those supporting a more Islamist approach against other Muslims in the country. ...

And:

5. Egypt stands out among Muslim-majority countries as having low tolerance of religious pluralism

While Egypt is home to some of the most intense government restrictions on religion, these restrictions are coupled with a Muslim public that is considerably less tolerant of religious pluralism than Muslims elsewhere, according to a recent Pew Research analysis. ...

* Like many Muslim publics surveyed around the world, a majority of Egyptian Muslims (74%) want sharia, or Islamic law, enshrined as the official law of the land. However, Egypt is one of the few countries where a clear majority (74%) of sharia supporters say both Muslims and non-Muslims in their country should be subject to Islamic law. Worldwide, a median of 39% of Muslims who favor enshrining Islamic law say sharia should apply to Muslims and non-Muslims alike.

* Egyptian Muslims also back criminalizing apostasy, or leaving Islam for another religion. An overwhelming majority of Egyptian Muslims (88%), say converting away from Islam should be punishable by death. Among the 37 countries where the question was asked, a median of 28% of Muslims say apostates should be subject to the death penalty.

As I have noted at GetReligion and at Scripps Howard, it is highly unlikely that the Egyptian conflict fades because a clear majority of the nation's population WANTS a state that applies sharia to all Egyptians. This majority would have to include many in the coalition that currently opposes the Muslim Brotherhood.

So why to Coptic Christians have so little faith in the police and soldiers who are supposed to be protecting their homes, businesses and sanctuaries?