Last week, GQ magazine dubbed Tony Blair philanthropist of the year for his global charity network, Faith Foundation.

Unfortunately, the Middle East's peace envoy did not have long in which to bask in a rare moment of public approval. Soon after, it was announced that plans for a partnership between his charity and Harvard Divinity School have come to naught. Harvard has withdrawn, saying, with chilling froideur, that "the aims of both organisations would be better served independently".

Was it something he said? You bet. In an article on the foundation's website, Blair, a committed Christian, predicted that the most dangerous and epic battles in the 21st century would be caused by religious extremism. Perhaps unsurprisingly, Harvard balked at this, and severed the link. In so doing it simply bolstered the former prime minister's idea that religion and its interpretation is a perpetual source of conflict and anger.

Much as it irks me to agree with Blair, he has a point. When I was at school, we were told that the wars of the next millennium would be created by dwindling supplies of water, oil and food, as populations grew and the planet got hotter. Looking at headlines in recent years, however, be they from Gaza or Syria, Northern Africa or Iraq, no-one surely can doubt that while oil, water and food are a source of growing friction, it is religious fanatics who pose most danger. Their hardline, heartless beliefs spread hatred across the map. Most terrifying of the new extremists is Isis, or Islamic State, whose intolerance and love of terror are horrifying.

No wonder there was outrage when a young and privileged Glaswegian joined Isis. Aqsa Mahmood's betrayal of her family's quiet Muslim values is deeply shocking, particularly as it coincides with news of the plight of David Haines, the aid worker from Scone, whose fate lies in these terrorists' hands. Like their fellow radical Islamists, Boko Haram in Nigeria, the beliefs of Isis are alien to anyone with an ounce of humanity. Are such people really religious, in the sense we understand it now, or is their creed merely a convenient banner under which to rally support?

Sadly, I don't think they can be dismissed as paying lip-service to faith. Their desire to create a global caliphate is firmly based in scripture, albeit an intemperate interpretation of it. Most Muslims are as low key as kirk-goers in their beliefs, but in the early middle ages, the land-grabbing and pillaging of Muslim warriors helped cast Europe into the so-called dark ages. Christian history, meanwhile, has been as much about conquest and subjugation, punishment and prejudice as about life-enhancing spirituality. As for the killings committed today by Jews and Arabs in the Middle East, it is like reading a book of medieval history, so little have attitudes changed.

One cannot say that historic wars fought in God's name were religiously motivated, but that the campaigns of extremists today are not. They are just as driven by a bloodthirsty creed as those behind the Spanish Inquisition or the Covenanters' slaughter. The irony of our times is that, although many of us are sceptical about theological certainty, or disillusioned by the institutions that represent it, we are equally loath to believe that anyone who commits torture and murder in the name of faith is rational. We prefer to think of them as mentally ill or brain-washed. How else to explain the burning of old women as witches in centuries past, or the dreadful way women are treated by fundamentalists across the world today?

And even if we do conclude that our vicious forebears were indoctrinated, how do we describe the motivation of peaceful practitioners of these same religions, across all ages including our own? Only a tiny minority of believers can be dismissed as unstable or sick, cowed or credulous.

The unpalatable and very frightening truth is that for those seeking power or land, riches or revenge, primitive religious conviction offers the language and the framework to make them strong. Doctrinal rules quell all doubts or compassion. Even more alarming is that the unthinking assurance of fanatics comes from an unfathomable region of the human mind, a place where unsophisticated belief and violence go hand in hand, with devastating consequences. Tony Blair has made many mistakes, but on this subject, history might well prove him right.