The line about the American general meeting the Arab Christian isn't as familiar as it should be. "When did your family convert?" the general asked. "About 2,000 years ago," the Arab answered wryly.

The general's ignorance is widely shared. Take but one example from closer to home. Over-zealous teachers in London have recently been pulling Syrian Orthodox refugees out of school assemblies in London, on the basis that Arab children must by definition be Muslims. The truth, of course, is that Christianity is an import from the Middle East, not an export to it. Christians have formed part of successive civilisations in the region for many centuries – they were, as Rowan Williams has pointed out, a dominant presence in the Byzantine era, an active partner in the early Muslim centuries, a long-suffering element within the Ottoman empire and, more recently, "a political catalyst and nursery of radical thinking in the dawn of Arab nationalism".

Today, though, the religious ecology of the Middle East looks more fragile than ever, as the Arab spring gives way to Christian winter. Ignorant western assumptions about cultural uniformity are mirrored by Islamists bent on purging other faith groups from their lands. Such intolerance has grown steeply since 9/11 of course, but its roots long predate the disastrous policies of George W Bush.

In Egypt, large numbers of Coptic Christians have moved abroad in response to a tide of discrimination and outright oppression. Though still numbering at least 5.1 million of an 80 million-strong population (according to government estimates disputed by the Coptic church), Copts face many professional glass ceilings, and scores of their churches have been attacked by Salafist extremists. About 600,000 Copts – more than the entire population of Manchester – have left their homeland since the early 1980s. If Mohamed Morsi's new constitution is implemented, the second-class status of Christians will be set in stone. Egypt will stagnate still further in consequence.

The catastrophe faced by Iraq's Christians is more widely recognised in the west, partly because of the media spotlight on individual tragedies, such as the storming of Baghdad's Syrian Catholic cathedral two years ago. More than 50 people were killed, and scores of others maimed, when al-Qaida-linked militants hurled grenades into the building before shooting worshippers at random. In 1990 there were between 1.2 and 1.4 million Christians in the country. Today, it is estimated that fewer than 500,000 remain.

The current conflict in Syria has placed Christians in the eye of yet another storm. Despite its brutality, the Assad regime guaranteed freedom of worship to minorities before the outbreak of civil war. This year, though, tens of thousands of Christians have fled from cities such as Homs and Qusayr in the face of Islamist rebels. The traditional Christmas market and lights in Qatana are now things of the past, because Islamist militias want all traces of Christian life to be erased. Their threats are anything but idle. On 25 October, Father Fadi Haddad, parish priest of St Elias's Greek Orthodox Church in the town, was found dead beside a road near Damascus. He'd been abducted several days beforehand after seeking to negotiate with the kidnappers of a local Christian dentist.

Even in notionally progressive Middle Eastern societies such as Turkey, anti-Christian discrimination is extensive, and "apostates" – former Muslim converts to Christianity or other faiths – face heavy penalties. Elsewhere in the Muslim world, this problem is yet more severe. The apostate is at real risk of death in Saudi Arabia and Iran. In Bahrain, Jordan, Kuwait, Qatar, Oman and Yemen, apostates risk punishments including the loss of property and the annulment of a marriage, "honour" killings by family members, detentions, imprisonment, torture and physical intimidation.

Why is all this so under-reported? This answer is simple: Christians rank low in an unacknowledged hierarchy of victimhood. Young Christians in the west don't become radicalised in support of their fellow believers, and persecuted Christians rarely respond with terrorist violence. This also tends to render their plight less newsworthy in the media eyes.

The truth about religious oppression – that it is Christians who are targeted in greater numbers than any other faith group on earth – thus comes as a surprise to many. A survey from 2007 found that some 200 million believers, or 10% of the global total, are threatened by discrimination or harassment or outright violence. The problem extends well outside Islamic countries to include India, the communist world, and even to Buddhist-majority societies such as Burma and Sri Lanka.

To some secularists, of course, these statistics are simply proof of religion's status as a malign force. But this is to overlook several critical points. Among them are that faith is often used as a figleaf for what are really political disputes and turf wars (take Nigeria, for example), and that Christianity and Islam, especially, are massive sources of social capital. On the positive side, faith-based conviction has mobilised millions to oppose authoritarian regimes, inaugurate democratic transitions, support human rights, and relieve human suffering.

Given that religion is not going to fade away, whatever the extent of secularisation in an untypical country such as Britain, the core priority should be freedom of conscience. This is not only a good in itself – religious liberty is the canary in the coalmine for freedom more generally.