Some say this was a case of naivety, of a scholarly theologian stumbling into the glare of a global media storm, blinking with surprise at the outrage he had inadvertently triggered. The learned man's thoughtful reasoning, say some, has been misconstrued and distorted by troublemakers, and the context ignored.

But such explanations are unconvincing. This is a man who has been at the heart of one of the world's multinational institutions for a very long time. He has been privy to how pontifical messages get distorted and magnified by a global media. Shy he may be, but no one has ever before accused this pope of being a remote theologian sitting in an ivory tower. On the contrary, he is a determined, shrewd operator whose track record indicates a man who is not remotely afraid of controversy. He has long been famous for his bruising, ruthless condemnation of those he disagrees with. Senior Catholic theologians such as the German Hans Kung are well familiar with the sharpness of his judgments.

But in the 18 months since Benedict was elected, the wary critics who have always feared this man were lulled into believing that office might have softened his abrasive edges. His encyclical on love won widespread acclaim and the pronouncement on homosexuality being incompatible with the priesthood (and its inference that homosexuals were to blame for the child sex abuse problems in the church) were explained away as an inheritance from Pope John Paul II's reign.

But while the Pope has tried to build a more appealing public image, what has become increasingly clear is that this is a man with little sympathy or imagination for other religious faiths. Famously, the then Cardinal Ratzinger once referred to Buddhism as a form of masturbation for the mind - a remark still repeated among deeply offended Buddhists more than a decade after he said it. Even his apology at the weekend managed to bring Jews into the row.

In fact, Pope Benedict XVI's short papacy has marked a significant departure from the previous pope's stance on interreligious dialogue. John Paul II made some dramatic gestures to rally world religious leaders, the most famous being a gathering in Assisi of every world faith, even African animists, to pray for world peace. He felt keenly the terrible history of Catholic-Jewish relations, and having fought with the Polish resistance to save Jews in the second world war, John Paul II made unprecedented efforts to begin to heal centuries of hostility and indifference on the part of the Catholic church to Europe's Jews. John Paul II also addressed himself to the ancient enmity between Muslims and Catholics; he apologised for the Crusades and was the first Pope to visit a mosque during a visit to Syria in 2001.

In contrast, Pope Benedict has managed to antagonise two major world faiths within a few months. The current anger of Muslims is comparable to the anger and disappointment felt by Jews after his visit to Auschwitz in May. He gave a long address at the site of the former concentration camp and failed to mention anti-semitism, and offered no apology - whether on behalf of his own country, Germany, or on behalf of the Catholic Church. He acknowledged he was a "son of the German people" ... "but not guilty on that account"; he then launched into a highly controversial claim that a "ring of criminals" were responsible for nazism and that the German people were as much their victims as anyone else. This is an argument that has long been discredited in Germany as utterly inadequate in explaining how millions supported the Nazis. Given his own involvement in the Hitler Youth movement as a boy, and his refusal to make a clean breast of the Vatican's acquiescence in the horrors of Nazism by opening its archives to historians, this was a shabby moment in Catholic history. Not for this pope those dramatic, epoch-defining gestures that made the last Pope such a significant global figure.

Even worse, in his Auschwitz address, he managed to argue in a long theological exposition that the real victims of the Holocaust were God and Christianity. As one commentator put it, he managed to claim that Jews were the "themselves bit players - bystanders at their own extermination. The true victim was a metaphysical one." This theological treatise bears the same characteristics as last week's Regensburg lecture; put at its most charitable, they are too clever by half. More plainly speaking, they indicate a deep arrogance rooted in a blinkered Catholic triumphalism which is utterly out of place in the 21st century.

But if his visit to Auschwitz disappointed many and failed to resolve outstanding resentments about the murky role of German Catholicism, this latest incident seems even worse. Quoting Byzantine emperor Manuel II Paleologos, he said: "Show me just what Muhammad brought that was new and there you will find things only evil and inhuman, such as his command to spread by the sword the faith he preached." It was a gratuitous reawakening of the most entrenched and self-serving of western prejudices - that Muslims have a unique proclivity to violence, a claim that has no basis in history or in current world events (a fact that still eludes too many westerners). Even more bewildering is the fact that his choice of quotation from Manuel II Paleologos, the 14th-century Byzantine emperor, was so insulting of the Prophet. Even the most cursory knowledge of dialogue with Islam teaches - and as a Vatican Cardinal, Pope Benedict XVI would have learned this long ago - that reverence for the Prophet is a non-negotiable. What unites all Muslims is a passionate devotion and commitment to protecting the honour of Muhammad. Given the scale of the offence, the carefully worded apology, actually, gives little ground; he recognises that Muslims have been offended and that he was only quoting, but there is no regret at using such an inappropriate comment or the deep historic resonances it stirs up.

By an uncanny coincidence the legendary Italian journalist Oriana Fallaci died last week. No one connected the two events, but the Pope had already run into controversy in Italy by inviting the rabid Islamophobe to a private audience just months ago. This is the journalist who published a bestseller in 2001 which amounted to a diatribe of invective against Islam. This is the woman who was only too happy to fling out comments such as "Muslims breed like rats" and "the increasing presence of Muslims in Italy and Europe is directly proportional to our loss of freedom." At the time of her papal audience, Fallaci's ranting against Islam had landed her in court and there was outrage at the Pope's insensitive invitation. The Pope refused to backtrack and insisted the meeting was purely "pastoral".

Put last week's lecture in Bavaria and the Fallaci audience alongside his vocal opposition to Turkish membership of the EU, and the picture isn't pretty. On one of the biggest and most volatile issues of our day - the perceived clash between the west and the Muslim world - the Pope seems to have abdicated his papal role of arbitrator, and taken up the arms in a rerun of a medieval fantasy.

An elderly Catholic nun has already been killed in Somalia, perhaps in retaliation for the Pope's remarks; churches have been attacked in the West Bank. How is this papal stupidity going to play out in countries such as Nigeria, where the tensions between Catholics and Muslims frequently flare into riots and death? Or other countries such as Pakistan, where tiny Catholic communities are already beleaguered? Or the Muslim minorities in Catholic countries such as the Philippines - how comfortable do they feel this week?

Two lines of thought emerge from this mess. The first is that the Pope's personal authority has been irrevocably damaged; how now could he ever present himself as a figure of global moral authority and a peacemaker after this? At the weekend, a message was read out from Cardinal Murphy O'Connor at all masses in Catholic churches in England; he spoke of the regret at any offence caused and urged good relations between Catholics and Muslims. For a church that prides itself on taking centuries to respond, this was unprecedented crisis management. It cannot but damage the pope's authority with the faithful that such emergency measures were necessary, and it compromises not just this pope but the papal office itself. (This is a job, after all, that is supposed to be divinely guided and at all times beyond reproach: a claim that looks a bit threadbare after the past few days.)

The second is a more disturbing possibility: namely, that the Catholic church could be failing - yet again - to deal with the challenge of modernity. In the 19th and 20th centuries, it struggled to adapt to an increasingly educated and questioning faithful; now, in the 21st century, it is in danger of failing the great challenge of how we forge new ways of accommodating difference in a crowded, mobile world. The Catholic church has to make a dramatic break with its triumphalist, bigoted past if it is to contribute in any constructive way to chart this new course. John Paul II made some dramatic steps in this direction; but the fear now is that Pope Benedict XVI has no intention of following suit, and that he has another direction altogether in mind.

More from Pope Benedict

On homosexuality
"Although the particular inclination of the homosexual person is not a sin, it is a more or less strong tendency ordered toward an intrinsic moral evil; and thus the inclination itself must be seen as an objective disorder. Therefore special concern and pastoral attention should be directed toward those who have this condition, lest they be led to believe that the living-out of this orientation in homosexual activity is a morally acceptable option. It is not."

On Buddhism
"Auto-erotic spirituality."

The ordination of women
On the excommunication of seven women who called themselves priests: "... the penalty imposed is not only just, but also necessary, in order to protect true doctrine, to safeguard the communion and unity of the church, and to guide consciences of the faithful."

On same-sex marriage
"Call[s] into question the family, in its natural two-parent structure of mother and father, and make[s] homosexuality and heterosexuality virtually equivalent, in a new model of polymorphous sexuality."

On rock music
"[A] vehicle of anti-religion"; "the complete antithesis of the Christian faith in the redemption."

On cloning
"[A] more dangerous threat than weapons of mass destruction."