As church after church is put to the torch in Egypt by members of the Muslim Brotherhood and its allies, one of the things that is going up in flames is the reputation of President Obama.

In the past 48 hours alone, some 57 Egyptian churches have been burned to the ground in the Nile valley. It will not be lost on the Egyptians that Mr. Obama has spent the crisis playing golf at Martha’s Vineyard.

Scores of Christians are being consumed in this conflagration, some burned beyond recognition defending their churches, even as Mr. Obama’s much-despised envoy in Egypt, Ambassador Patterson, still tries to effect a reconciliation between the the Muslim Brotherhood conducting this devastation and the Egyptians who revolted against the Brotherhood’s rule.

Mr. Obama came out against a pastoral background to urge the Egyptian military and government to take it easy on his favored Islamists and to hint at even more sanctions if they do not. As Mr. Obama retreated back to the beach, his aides warned of a cutoff of the $1.5 billion a year that American has been providing, though such aid is now being overwhelmed with a package of $12 billion that began flowing from Saudi Arabia, Kuwait and the United Arab Emirates only last month.

In Arab culture, such language and mannerism, including the wagging of fingers, will be seen as insulting, which at least partly explains the rush by the oil-rich countries to help the revolutionary government in Cairo. Yet America’s problem is larger than finger pointing. The Obama administration is allying itself against those fighting for a secular Arab world, a fight that is now arising across the Arab world. It may be that two decades ago the radical religious ideology of the Muslim Brotherhood won some adherents. But Arabs have long since rejected that siren. America seems to have trouble catching up.

Enters Egypt, by far the largest and most influential nation. It is a cultural and intellectual soft power, never comfortable with what the Muslim Brotherhood sought to impose under President Morsi. Egypt’s 14 million Christians, descendants of the pharaohs peacefully nestled for centuries among a vast Muslim population found themselves singled out, yet again. It happened many times over the past 14 centuries ever since Muslims invaded Egypt and forcibly converted most of the population, except for those stubborn Coptic Christians who took the pain, but kept their faith.

Coptic is the Pharoes’ name for “Egyptian,“ a little appreciated echo of the fact that all of Egypt was once a Coptic, Christian nation — for a full seven centuries until the Islamic invasion in the seventh century of the common era. It has kept many of those beliefs, assembled mostly around co-existence and absorption as invaders came and went.

Romans, Macedonians, Persians, Christians, Muslims, Ottomans, French and Brits, all traversed the Valley of the Nile, but the essence of Egypt remained deeply Egyptian long after they left. This is the context in which the battle with the Muslim Brotherhood has erupted.They are basically waging a war against the essense of Egypt shared by the majority of the country’s 86 million citizens, both Muslims and Christians. The Brotherhood’s loss, which took a year, was predictable.

When in 2009 President Obama came to Cairo for his first major speech on foreign affairs, he simply made his remarks and walked away, thinking his “Islamist friendship message,“ coupled with his charisma, would be enough. He ignored the Christian Arabs, who have been the bridge between Western and Arab cultures since the 17th century — translators of the greatest works of arts, literature, civilization, theater, and cinema. They, as did Jews living in the Arab world, made an outsized contribution to whatever success has been made toward modernity.

The eviction of the Christians from the Arab world, as the eviction of the Jews before them, is a loss not only for the West but mostly for Arab Muslims. More importantly, it is a crime against humanity. Where is President Obama? Will his silence make him a partner in this crime?