When Pope Benedict XVI met American Jewish leaders this morning, one Vatican prelate was a notable absentee: Dario Castrillón Hoyos, the Colombian who spent years negotiating the return to the fold of excommunicated ultra-conservative Lefebvrist Catholics, including the now famous (or notorious) Bishop Richard Williamson, who denies the murder of millions of Jews in Nazi gas chambers.

The white-haired, mild-mannered Castrillón Hoyos has become the scapegoat for the debacle that followed. He turns 80 in July, they whisper in the Vatican, and he pushed the German Pope into rehabilitating the excommunicated bishops so that he could retire declaring “mission accomplished”.

But it won't wash. No one pushes a Pope into anything, least of all this one. Few Popes have been as sure of themselves, or their mission, as the former Cardinal Joseph Ratzinger, distinguished theologian and former “enforcer” of Vatican doctrine.

The Vatican says that the Pope was unware of Williamson's views, and we must accept that. But as Salomon Korn, vice-president of the Central Council of Jews in Germany, remarked to Der Spiegel: “The Pope had to have known whom he was pardoning. After all, he's a man of intelligence with profound knowledge.”

It is not just the Holocaust, after all: the Lefebvrists rejected (and many of them still reject) the Second Vatican Council, which among other reforms absolved the Jews of blame for the death of Christ and defined them as “our older brothers”.

Angela Merkel, the German Chancellor, who took the unprecedented step of rebuking the German Pope, has made her peace with him. The Chief Rabbinate of Israel, which cancelled a meeting with the Pope in March, appears to have changed its mind. The Pope's trip to Israel in May is back on the agenda.

The furore, however, follows a series of papal gaffes: the 2006 speech in Regensburg (his alma mater) describing Islam as inherently violent and irrational, the wounding dismissal of Protestant denominations as “not proper churches”, the reinstament of a Good Friday Latin prayer calling for the conversion of the Jews.

As the American Vatican watcher John Allen puts it, there is a pattern: the Pope “says or does something obviously destined to set off fireworks”, the Vatican appears surprised by the reaction, and there follows belated damage control.

So who is to blame? The easy answer (apart from Castrillón Hoyos) is that the Vatican media operation — headed by a likeable Jesuit priest, Father Federico Lombardi — is incapable of handling, let alone heading off, public relations disasters. Father Lombardi himself observed this week that the Vatican should improve the way it handles “hot topics”.

But this won't wash either. True, the PR could do with an overhaul, but the Holy See is an absolute monarchy, in which everything comes from the top. Not all autocrats rule in the same way: Benedict is more isolated than some Popes. He only sees a handful of close advisers, and unlike John Paul II does not have people from all walks of life to meals.

He is shy, thoughtful, compassionate, deeply spiritual — quite the opposite of the caricature of the Panzerkardinal or “God's Rotteweiller” that was created when he ran the Congregation for the Doctrine of the Faith for two decades on behalf of John Paul II.

His first encyclical was on love, human and divine: his next is on the plight of the poor in a globalised world. He recently reached out to young people, rightly warning them not to mistake virtual online friendship for the real thing. His homilies are often moving, and always rewarding. He has shown an open mind on Darwin, on Galileo, even on Martin Luther.

But his priority, as he made perfectly clear on the eve of his election, is to safeguard the Catholic faith in a world of growing secularism, hedonism, triviality, materialism and challenges from other faiths such as Islam. He has revived the Tridentine Mass, and said recently that inter-faith dialogue was not possible in the “strict sense of the term”.

Not encouraging words for Muslims, Jews, or indeed other Christians. Whether the Benedict approach is the right one for the Church in the 21st century is an open question. But the cardinals cannot say that they didn't know what they were getting when they chose him nearly four years ago.

Times Recommends

• 'Radio Rancid' is scourge of Obama
• French gulp as global warming alters wines
• Colton, the barefoot boy bandit, outfoxes sheriffs