I HAVE spent much of the past three years writing Christianophobia  (Rider Books), a chronicle of discrimination and persecution faced by Christians around the world. Two points were clear from the start. First, that much anti-Christian prejudice and violence - in China, India, Vietnam, North Korea, Burma, Sri Lanka, Cuba, or Israel, among other places - has nothing to do with militant Islam; and, second, that a number of grievances felt by Muslims are reasonable.

For example, I believe (in line with the clearly broadcast views of most church leaders around the world) that the Iraq invasion of 2003 was a serious mistake, and have a keen sense of the West's part in promoting the sense of injustice felt by many Arabs in particular.

Nevertheless, of the 13 societies I surveyed in detail, seven have Muslim majorities or large Muslim populations. This obliged me to confront a sensitive but critical question. Is there a problem with Islam as such, or is the trouble more a matter of contingencies? (After all, large parts of the Christian world were saturated with unsurpassed levels of violence 70 or 100 years ago.)

Part of the answer to this question is theological. There is a theory that the idea of jihad is more deeply embedded in Islam than related notions in the other world religions - and therefore that Islam is more susceptible to violent extremism - because of the martial context in which Islam took root.

It does not help that, for the first half of the Muslim era, Muslims thought of themselves as being on top, both culturally and in terms of military power, for understandable reasons.

Defence advocates tend to reply that the Prophet Muhammad's ministry took place in a hostile context, and that Islam's matrix was connected with the need to defend the community against dangerous opponents from the start. Supporters of this argument can sometimes turn the tables on Christianity by suggesting that, although the New Testament is saturated in the language of peace, Christ's followers would in time become extremely violent towards non-Christians and perceived heretics.

Thousands of "witches" were murdered in early modern Europe and America; Thomas Aikenhead was executed in Scotland for blasphemy as recently as 1697. This is to say nothing of earlier inquisitions, or of the anti-Jewish pogroms that took place later in Christian societies.

Nor is Christian-backed violence a thing of the past. In the 1970s and '80s, Lebanese Phalangist militias were dominated by Maronites in communion with the see of Rome. During the '90s, Orthodox Christians (and former Communists who used their religious heritage as a flag of convenience) were guilty of extreme aggression against Muslims and Roman Catholics in the Balkans.

AS WITH the Bible, selective quotations from the Qur'an are unlikely to advance the discussion: it contains both the aggressive-seeming "sword" verse (9:5 - "When the sacred months are over slay the idolaters wherever you find them. Arrest them, besiege them, and lie in ambush everywhere for them. If they repent and take to prayer and render the alms levy, allow them to go their way. God is forgiving and merciful") and the tolerant-seeming "Let there be no compulsion in religion" (2:256), which is traditionally seen as underlining the right of non-Muslims to convert freely.

A more solid account of the Muslim position would focus on its concentric understanding of faith, with Islam at the centre; Jews and Christians, so-called People of the Book, in an intermediate position; and the representatives of shirk (polytheism) and kufr (those who reject religion out of ingratitude) at the edge.

I have noted that in Muslim polities, Jews and Christians were traditionally given the status of dhimmis. They paid a special tax and enjoyed qualified rights. Notwithstanding the inequality of this relationship - and, of course, its monotheistic bias - it is reasonable to hold that the dhimma arrangement was a precursor of the public international law that did not evolve in Europe until the early-17th century.

Another important consideration is that some Muslim jurists were prepared to extend the definition of People of the Book to cover Hindus, because of the scriptural status of the Bhagavad Gita. The Mughal empire had an enormous non-Muslim population of Hindus and others.

CHRISTIANITY's trajectory has been very different. It did not develop a formal understanding of interfaith toleration, despite the ethic of radical self-giving love towards all that is set out in the Gospels. Landmarks in the history of Europe such as the Treaty of Westphalia (1648) are reminders of how long it took for the principle of toleration to be accepted even between the Christian denominations.

Nevertheless, as the anthropologist Jonathan Benthall has suggested in an important essay on the history of religious toleration, Christianity eventually became more self-critical - and subversive of its own apparent strictness - than Islam. One fruit of Jesus's special emphasis on the poor and marginalised has been a tradition of positive discrimination in the modern era.

In Islam, the right to criticise the dominant faith rarely extends to the forces of shirk and kufr who are condemned so comprehensively in the Qur'an. It is also significant that Islam never evolved into movements analogous, say, to Liberal, Reform, and Orthodox Judaism.

Muhammad Abduh (1849-1905), a Grand Mufti of Egypt, and Muhammad Iqbal (1877-1938), who ministered in what is now Pakistan, were two significant reform-minded thinkers whose ideas failed to take wing. Today, Christians and others are surely right in calling on liberal Muslim intellectuals to show greater robustness in confronting awkward questions, including the crisis of institutional authority in Islam.

Yet, as Benthall emphasises, the situation should not be considered static. The lesson of the past is clear:

Islam has proved to be just as flexible as Christianity in accommodating popular forms of belief and practice. Second, its scholars were able to recognise Hindus as People of the Book, though on most objective criteria they would have fallen more naturally into the category of shirk. If this leap of toleration could be made for the Hindus, albeit for reasons of state, why not today for other belief systems such as the indigenous cosmologies of Africa, Indonesia and Malaysia?

From "Confessional Cousins andthe Rest" in Anthropology Today,  February 2005

Just as Christianity has evolved, then, there are reasonable grounds for thinking that Islam will do so, too. It seems right to finish on an eirenic note by emphasising that the points of contact between the two traditions are at least as significant as the differences. When they are true to their guiding principles, both faiths insist on the sanctity of the person as a seeker of God, and from this should duly follow a recognition of religious freedom as the first of human rights.

Whether this awareness will spread is not for me to predict. For the Christian, it is hope - not more malleable impulses towards either optimism or pessimism - that really counts. Hope, in St Augustine's resonant words, "has two beautiful daughters: their names are anger and courage. Anger that things are the way they are. Courage to make them the way they ought to be."

Rupert Shortt is Religion editor of The Times Literary Supplement, and a Visiting Fellow of Blackfriars Hall, Oxford.

This is an edited extract from Christianophobia: A faith under attack, published by Rider at £20 (CT Bookshop £18); copyright © Rupert Shortt 2012.