Nazareth.

When Pope Benedict XVI visited the Holy Land five years ago, Israel heightened its security, gladly emphasising the potential threat he supposedly faced in Israel from Muslim extremists.

As his successor, Pope Francis, arrived in Israel late on Sunday, security was no less strict. Some 9,000 police had been drafted in to protect him, Christian institutions were under round-the-clock protection, and the intelligence services were working overtime. According to a Vatican official, Israel’s preparations had turned “the holy sites into a military base”.

On this occasion Israel was less keen to publicise the source of its fears, because the most tangible threat came not from Islamists but Jewish fanatics linked to Israel’s settler movement.

Last month they issued a death threat to the Roman Catholic Bishop of Nazareth and his followers, while recent weeks have seen clergy attacked, churches and monasteries defaced with offensive graffiti, and cemeteries desecrated.

The building where the Pope was due to meet Israeli prime minister Benjamin Netanyahu today was daubed with “Death to Arabs and Christians”. Last Friday, a church in the city of Beersheva was sprayed with “Jesus is a son of a bitch”.

Israeli police have arrested or issued restraining orders on several dozen Jewish extremists in the past few days.

Fouad Twal, the Latin Patriarch of Jerusalem, has warned that “acts of unrestrained vandalism are poisoning the atmosphere”.

Indeed, the mood of intolerance has spread beyond a dangerous fringe. Hundreds of Israeli Jews demonstrated angrily in Jerusalem last week against the Pope, while police barred Catholic authorities from putting up banners celebrating his visit, apparently fearful it could trigger wider protests.

The local Palestinian Christian population, both in the occupied territories and inside Israel itself, is feeling more embattled than ever – and not just from settlers.

In Bethlehem on Sunday the Pope made an unscheduled stop to pray at the monstrous concrete wall that has turned Jesus’ birthplace into a prison for its modern inhabitants. At a nearby refugee camp he was reminded that Israel bars residents from ever returning to homes now in Israel.

Meanwhile, Netanyahu has provided his personal backing to a plan whose barely concealed goal is to divide the large Palestinian minority inside Israel – pitting Christian against Muslim – by seeking to draft the former into the Israeli military.

Despite this Pope’s popularity, there have been rumblings of dissatisfaction at his priorities on this brief, three-day trip.

The official purpose is to mark the 50^th anniversary of a meeting in Jerusalem between Pope Paul VI and Patriarch Athenagoras that ended of a 1,000-year schism between Rome and the Orthodox Church.

The Vatican has emphasised that Francis’ trip is “absolutely not political”. His itinerary, which did not include time for a visit to the Galilee, where most Palestinian Christians are located, suggested the Pope was not likely to offer his flock solace beyond the general hope he expressed in Bethlehem for a “stable peace” in the region.

The Holy Land’s Christians are an increasingly vulnerable minority. Inside Israel, for example, their proportion has fallen from nearly a quarter of the Palestinian minority in the early 1950s to just 10 per cent today. A similar decline has taken place in the occupied territories.

Although Israel blames Muslim fanaticism for this decades-long trend, the truth is different. In repeated surveys, only a small minority of Christians blame Muslims for the exodus.

In part, the proportion of Christians has fallen over time simply because of their tendency to smaller familes than Muslims. But equally significant are Israel’s oppressive twin policies of belligerent occupation in the West Bank, Gaza and East Jerusalem and a political system of exclusive Jewish privilege inside Israel.

All Palestinians, Muslim and Christian alike, have been harmed by Israeli rule. But Christians have been better able to exploit connections to Western communities, giving them an easier passage out.

None of this fits well with Israel’s narrative of a clash between the Judeo-Christian world and Islam, or its desire to present itself as a unique haven as neighbouring Arab states sink into sectarian conflict. On Sunday Netanyahu claimed Israel was the only Middle East country to offer “absolute freedom to practice all religions”.

The reality, however, is that the settlers’ violence feeds off a religious and ethnic intolerance cultivated on many fronts by the Israeli state itself.

It starts early, with a majority of Jewish children educated in religious schools that scorn a modern curriculum. Instead they drill into pupils literal interpretations of the Bible that encourage Jewish chauvinism.

Israel’s programme of Holocaust education rejects universal lessons, preferring to nurture a sense of Jews as history’s eternal victims. Many Israelis believe they should be constantly on guard – and armed – against a world of anti-semitic gentiles.

Hardline Orthodox rabbis, given control over large areas of Israeli life, have become the sole arbiters of moral values for many Israelis.

The government’s latest effort to pass legislation affirming Israel as the “nation-state of the Jewish people” is designed to stymie any hope of a multi-cultural future.

And finally, decades of rule over Palestinians have been exploited by Israel to invest ever greater Jewish religious symbolism in contested or shared holy places, most notably the al-Aqsa mosque compound in Jerusalem. Slowly a territorial conflict is gaining the attributes of a religious war.

Local church leaders understand this well. In the run-up to the Pope’s visit, Twal asked pointedly: “What effect is created by [an] official discourse on Israel being a state for one group only?”

The Pope noted in Jordan on Saturday that religious freedom was a “fundamental human right”. That is certainly a message Israel’s leadership needed to hear stressed when Francis met them today.

A papal visit that eschews politics to focus only on religion – elevating holy sites above the people who live next to them – betrays a Christian community that needs all the help it can get as it fights for its continuing place in the Holy Land.

Jonathan Cook won the Martha Gellhorn Special Prize for Journalism. His latest books are “Israel and the Clash of Civilisations: Iraq, Iran and the Plan to Remake the Middle East” (Pluto Press) and “Disappearing Palestine: Israel’s Experiments in Human Despair” (Zed Books).  His website is www.jonathan-cook.net.

A version of this article first appeared in the National, Abu Dhabi.