You can literally look up what happened on Wikipedia, but the short of it is Mongol invasions and Mamluk misrule. I mean two thirds of the population left, that shit got everyone (though it admittedly got Jews and Christians more). Then it was victim to more Ottoman misrule. Not saying these are good things, but speaking as a Muslim Middle Eastern guy the scathing hatred for Jews in the modern Middle East is unlike anything from before the 20th century, and the stereotypes you'll usually see (mainly the deceptive Jew that can't be trusted to hold a promise and Jews controlling the world) are direct results of Zionist actions.

Are we totally going to ignore the fact that the Mamluks and other Turks were foreigners who only had Islam to try to bond with the region they were taking over. It's not like it was Levantine Jews vs Levantine Muslims.

It's a lot like how the US helps Israel because it has the same western values despite religion.