It is a chilling five-minute film made by the Islamic State of Iraq and the Levant (Isis), showing its fighters stopping three large trucks on what looks like the main highway linking Syria and Iraq. A burly bearded gunmen takes the ID cards of the drivers who stand nervously in front of him.

“You are all Shia,” he says threateningly.

“No, we are Sunni from Homs,” says one of the drivers in a low, hopeless tone of voice. “May Allah give you victory.”

“We just want to live,” pleads another driver. “We are here because we want to earn a living.” The Isis man puts them through a test to see if they are Sunni. “How many times do you kneel for the dawn prayer?” he asks. Their answers vary between three and five.

“What are the Alawites doing with the honour of Syria?” rhetorically asks the gunman who by this stage has been joined by other fighters. “They are raping women and killing Muslims. From your talk you are  polytheists.” The three drivers are taken to the side road and there is gunfire as they are murdered.

The armed opposition in Syria and Iraq is today dominated by Salafi jihadists, fundamentalist Islamic fighters committed to holy war. Those killing non-Sunni drivers on the Damascus-Baghdad road are an all too typical an example of this. Western governments may not care very much how many Shia die in Syria, Iraq or Pakistan, but they can see that Sunni movements with beliefs similar to the al-Qa’ida of Osama bin Laden, today have a base in Iraq and Syria far larger than anything they enjoyed in Afghanistan before 9/11 when they were subordinate to the Taliban.

The pretence that the Western-backed and supposedly secular Free Syrian Army was leading the fight to overthrow President Bashar al-Assad finally evaporated last December as jihadists overran their supply depots and killed their commanders.

In the past six months there have been signs of real anger in Washington at actions by Saudi Arabia and the Sunni monarchies of the Gulf in supplying and financing jihadi warlords in Syria who are now so powerful. US Secretary of State John Kerry privately criticised Prince Bandar bin Sultan, head of Saudi intelligence since 2012 and former Saudi ambassador in Washington, who had been masterminding the campaign to overthrow the Assad government.

The film shows the Islamic State of Iraq and the Levant militants

The three Syrian truck drivers are pulled over

All three are killed for not being Sunni Muslims

He struck back by denouncing President  Obama for not intervening militarily in Syria when chemical weapons were used against civilians.

Last month, it was revealed that Prince Bandar, while remaining intelligence chief, was no longer in charge of Saudi policy in Syria. He has been replaced by interior minister Mohammed bin Nayef, who gets on with the US and is chiefly known for his campaign against al-Qa’ida in the Arabian Peninsula.

Prince Miteb bin Abdullah, son of the Saudi King Abdullah and head of the Saudi National Guard, will also play a role in formulating a new Syrian policy.  Saudi Arabia’s differences with some of the other Gulf monarchies are becoming more explicit, with the Saudis, Bahrain and the United Arab Emirates withdrawing their ambassadors from Qatar this month. This was primarily because of Qatar’s backing for the Muslim Brotherhood in Egypt, but also for its funding and supplying of out-of-control jihadi groups in Syria.  

Saudi Arabia took over from Qatar as the main funder of the Syrian rebels last summer. But Saudi involvement is much deeper and more long term than this, with more fighters coming from Saudi Arabia than from any other country. 

Saudi preachers call vehemently for armed intervention against Assad, either by individual volunteers or by states. The beliefs of Wahhabism, the puritanical literalist Saudi version of Islam, are not much different from those of al-Qa’ida or other Salafi jihadist groups in Syria, Iraq, Afghanistan, Pakistan, Egypt and Libya.

The Saudis have always ideologically opposed Shi’ism as a heresy, much as Roman Catholics in Reformation Europe detested and sought to eliminate Protestantism. This hostility goes back to the alliance between the Wahhabis and the House of Saud dating from the 18th century. But the key date for the development of the jihadist movements as political players is 1979, with the Soviet invasion of Afghanistan and the Iranian revolution, when Ayatollah Khomeini turned Iran into a Shia theocracy.

During the 1980s, an alliance was born between Saudi Arabia, Pakistan (or more properly the Pakistani army) and the US which has proved extraordinarily durable. It has been one of the main supports of American predominance in the region, but also provided a seed plot for jihadist movements of which Osama Bin Laden’s al-Qa’ida was originally only one strain.

The shock of 9/11 provided a Pearl Harbour moment in the US when public revulsion and fear could be manipulated to implement a pre-existing neo-conservative agenda by targeting Saddam Hussein and invading Iraq. A reason for waterboarding al-Qa’ida suspects was to extract confessions implicating Iraq rather than Saudi Arabia.   

The 9/11 Commission report identified Saudi Arabia as the main source of al-Qa’ida financing. But six years after the attack – at the height of US-al-Qa’ida military conflict in Iraq in 2007 – Stuart Levey, the Under-Secretary of the US Treasury in charge of monitoring and impeding terror financing, told ABC News that, when it came to al-Qa’ida, “if I could somehow snap my fingers and cut off the funding from one country, it would be Saudi Arabia.” He added that not one person identified by the US or the UN as funding terrorism had been prosecuted by the Saudis.

Despite this high-level frustration at the Saudis for not cooperating, nothing much had improved a couple of years later. US Secretary of State Hillary Clinton wrote in December 2009 in a cable released by Wikileaks: “Saudi Arabia remains a critical financial support base for al-Qa’ida, the Taliban, LeT [Lashkar-e-Taiba in Pakistan] and other terrorists groups.” She complained that in so far as Saudi Arabia did act against al-Qa’ida, it was as a domestic threat and not against its activities abroad.

The US Under-Secretary for Terrorism and Financial Intelligence, David Cohen, last week praised Saudi Arabia for progress in stamping out al-Qa’ida funding sources within its own borders, but said that other jihadist groups could access donors in the kingdom.

Saudi Arabia is not alone among the Gulf monarchies in supporting jihadists. Mr Cohen says sourly that “our ally Kuwait has become the epicentre for fundraising for terrorist groups in Syria”. He complains particularly of the appointment of Nayef al-Ajmi as both Minister of Justice and Minister of Islamic Endowments (Awqaf) and Islamic Affairs. He says: “Al-Ajmi has a history of promoting jihad in Syria. In fact, his image has been featured on fundraising posters for a prominent al-Nusra Front financier.” He adds that the Awqaf ministry has recently announced that fundraisers can now collect donations for the Syrian people at Kuwait mosques, opening the door wide to jihadist fundraisers.

A further point coming across strongly in leaked American diplomatic traffic is the extent to which the Saudis gave priority to confronting the Shia. Here the paranoia runs deep: take Pakistan, Saudi Arabia’s most important Muslim ally, of which a senior Saudi diplomat said that “we are not observers in Pakistan, we are participants”. Pre-9/11, only Saudi Arabia, Pakistan and the United Arab Emirates  (UAE) had given official recognition to the Taliban as the government of Afghanistan.

There is something hysterical and exaggerated about Saudi fear of Shia expansionism, since the Shia are only powerful in the handful of countries where they are in the majority or are a strong minority. Of 57 Muslim countries, just four have a Shia majority.

Nevertheless, the Saudis were highly suspicious of Pakistani President Asif Ali Zardari and made clear they would have much preferred a military dictatorship in Pakistan. The reason for the dislike was sectarian, according to UAE foreign minister Sheikh Abdullah bin Zayed who told the Americans that “Saudi Arabia suspects that Zardari is Shia, this creating Saudi concern of a Shia triangle in the region between Iran, the Maliki government in Iraq, and Pakistan under Zardari”.

Sectarian hostility to the Shia as heretics is combined with fear and loathing of Iran. King Abdullah continuously urged America to attack Iran and “cut off the head of the snake”. Rolling back the influence of the Shia majority in Iraq was another priority. Here was another reason why so many Saudis sympathised with the actions of jihadists in Iraq against the government.

The takeover of Iraq by a Shia government – the first in the Arab world since Saladin overthrew the Fatimid dynasty in Egypt in 1171 – had caused serious alarm in Riyadh and other Sunni capitals, whose rulers wanted to reverse this historic defeat. The Iraqi government noticed with alarm in 2009 that when a Saudi imam issued a fatwa calling on Shia to be killed that Sunni governments in the region were “suspiciously silent” when it came to condemning his statement.

The Arab uprisings of 2011 exacerbated sectarianism, not least in Saudi Arabia which is always highly conscious of its Shia minority in the Eastern Province. In March, 1,500 Saudi troops provided back up for the al-Khalifa royal family in Bahrain as they crushed pro-democracy protests by the Shia majority on the island, the openly sectarian nature of the clampdown underlined when Shia shrines were bulldozed.

In Syria, the Saudis believed that the Syrian government would be swiftly overwhelmed like that of Muammar Gaddafi. They underestimated its staying power and the support it was getting from Russia, Iran and Hezbollah in Lebanon. But Saudi involvement, along with that of Qatar and Turkey, de-emphasised secular democratic change as the ideology of the uprising, which then turned into a Sunni bid for power in which the Salafi jihadist brigades were the cutting edge of the revolt.

Predictably, the Alawites and other minorities feel they have no choice but to fight to the death.

Many nonsensical conspiracy theories have evolved, peddling the idea that the US government was somehow complicit in the 9/11 attacks. The very absurdity of these theories has diverted attention from the fact that in one sense there was a conspiracy, but it was quite open and never a secret.

The price of the triple alliance between the US, Saudi Arabia and Pakistan was the jihadi movement. So far, this is anti-Shia before it is anti-Western, but, as the Isis gunmen on the Damascus-Baghdad road showed, any non-Sunni is at risk.

Read more: Why the global 'war on terror' went wrong