It's a bit of everything.
The state of Israel came into existence during a period of intense violence in Palestine between Jews, Arabs, and British authorities. This coincided with an era of Arab Nationalism, in which many Arabs identified strongly with other Arabs and weakly with their nationality. many of these nations were only a few years old at this point; Jordan was born in 1946 and Israel 1948. Consequently the creation of the state of Israel was loathed by Arabs who regarded its existence as aggressive imperialism. The 1948 exodus of Palestinians from the new Israeli state is called the Nakba (disaster).
There's a linguistic aspect to this which should be noted. In the Arab world Israel is often regarded as illegitimate, in which case the occupier is often referred to as being 'Jewish' instead of 'Israeli'. This originates in the fact violence before the creation of the Israeli state was rightly summarised as being between Jews and Arabs. In refusing to accept the existence of an Israeli state, Israelis are simply regarded as Jews. This undoubtedly does not reduce anti-Semitic thinking.
However, the popularity of secular Arab Nationalism was not to last. Support for Arab Nationalism declined as the prospect of achieving Pan-Arabism collapsed. This ideology would be replaced by the rising tide of political Islam.
The Quran, like the Bible, is a big complex book with lots of seemingly conflicting ideas. There are anti-semitic elements in the Quran which relate to a period of early persecution against Muslims by pagan and Jewish tribes. This is often used as a legal basis for prejudice against non-Muslims by Islamist hardliners.
Saudi Arabia has been called out repeatedly for using textbooks which teach anti-Semitism. The US government criticised their textbooks in 2001 following the September 11th Attacks, arguing that these books may have contributed towards the hijackers beliefs. One tenth grade textbook on monotheism included statements like:
"The Hour will not come until Muslims will fight the Jews, and Muslims
will kill all the Jews."
In 2002 Al Fawzan, author of the book in question, rejected US demands:
"The Jews and Christians and the polytheists have shown their
heartfelt hatred and try to prevent us from the true path of God. They
want to change our religion and our teaching to disconnect us from
Islam so they can come and occupy us with their armies. It is bad
enough when it comes from the infidels, but worse when they are of our
skin. They say we create parrots, but they are the real parrots
repeating what our enemies say of Islam."
In 2006 Saudi authorities told their US counterparts that the reforms had been completed, but this was quickly brought into question when an investigation by Freedom House found textbooks with dubious content still in circulation.
The problem is that Saudi textbooks are not limited to use in Saudi Arabia, they have been distributed far and wide to mosques and schools with ties to Saudi Arabia. In 2010 a BBC investigation found books which included anti-Semitism were being used by some faith groups in the UK.
In 2012 Human Rights Watch founder Robert Bernstein criticised Saudi Arabia for continuing to print new textbooks which contained anti-Semitic content. Citing one eighth grade book:
"The Apes are the people of the Sabbath, the Jews; and the Swine are
the infidels of the communion of Jesus, the Christians."
A November 2018 report by the Anti Defamation League found that textbooks printed for the 2018-2019 academic year still contained questionable content.
“The hour will not come until Muslims fight the Jews, so that the
Muslims kill them, until the Jew hides behind rock and tree, so the
rock or the tree says: ‘Oh Muslim, oh servant of God, this Jew is
behind me, so kill him.’”
In 2014 Emile Nakhleh, former Director of the CIA's Political Islam Strategic Analysis Program, warned that the Islamic State's education system was very similar to Saudi Arabia's. He concludes that the consequence of Saudi education has been to encourage violence against non-Muslims, and notes the paradox of Saudi willing to consider peace on the basis of 1967 borders with a state which does not exist in Saudi textbooks.
Even the geography curriculum discusses the region from an Islamic
perspective. For example, kids are taught that the “Zionists” have
occupied Palestine illegally, and the Islamic umma one day must
re-establish Muslim control over Jerusalem, the “Third Qibla” of
Islam, to which Muslims turn to pray after Mecca and Medina.
“Israel,” for example, does not appear on maps of the Arab world in
Saudi geography textbooks.
The Saudi youth are socialized in public schools on the importance of
Islam in the personal, familial, social, and national levels. Whenever
Islam, as a faith and a territory, is threatened or invaded, Muslims
have a duty to do jihad against the perceived “enemies” of Islam.
Saudi education espouses this ideology, so do al-Qaeda and IS. In the
past three decades, Muslim youth have participated in large numbers in
jihad across the Muslim world, from Afghanistan to Chechnya, and from
the Balkans to Iraq and Syria.
The Saudi government participates in the anti-IS coalition, yet IS’s
jihadist ideology resonates with Saudi educated youth. Their
government talks about a possible peace with Israel should it withdraw
to the 1967 borders, yet Saudi youth do not see Israel on the maps in
If the Saudi youth are taught about the duty of jihad in the face of a
“war on Islam,” as Bin Ladin had preached for years, and view IS
rightly or wrongly as the “defender” of Islam, they can’t understand
why their government is fighting on the side of Islam’s “enemies.”
In conclusion, there are a variety of reasons why many Muslims exhibit prejudice against Jews. These relate most strongly to political reasons; Israeli and American behaviour in the Middle East. Conspiracy theorist Muslims believe, as do conspiracy theorist non-Muslims in America and Europe, that America is the puppet of a Jewish conspiracy. Religious reasons are rooted in parts of the Quran emphasised by Saudi religious authorities, who have used their wealth to spread this particularly intolerant version of Islam.
It seems unlikely that this prejudice would be as pronounced without numerous issues which plague the Middle East: widespread poverty, the corruption of secular institutions, Saudi patronage of Salafi Islam, the ongoing Israeli-Palestinian conflict, and American aggression in the region.