Supercessionism. The fact that we didn't convert to Christianity and rejected their messiah, puts doubt on their absolutism of being correct. i.e. Jesus's own people rejected him. Hence why they call the Hebrew Bible 'Old' Testament and speak of a 'New' covenant. They believe Judaism is old, obsolete, and meant to be replaced.
Deicide, Blood Libel. They blame Jews for killing Jesus even though it's pretty blatant in the New Testament that Romans crucified him. Yet since they didn't read for most of the existence of Christianity I suppose religious officials just claimed Jews did it. Every now and then a Christian child would die and then the Christians would use that as an excuse to raid/loot/beat/murder/rape/burn everything in a state sanctioned riot called a pogrom. Blood Libel is still around typically in the form of nebulous 'Palestinian Children' that Israel somehow kills every day that nobody can name or cite.
Stereotypes from the Middle ages. Christians forced Jews to live in walled sections of cities called Ghettos and set a curfew and of course Jews had to pay the guards that enforced the curfews. Limited what Jews could wear, what animal they can ride, what professions they could do, banned Jews from guilds and Universities. Then Christians accused Jews of being clannish and sticking together and separating themselves. Another favorite is blaming Jews for plagues or bad wells.
Jews don't fit into any nationalist program as Jews are a perpetual nation and only native to Israel. So if a nationalist government comes into power they tend to label Jews as outsiders and therefore bad.
Communists tend to want to destroy the concept of a nation state and don't like that Jews never gave up being Jewish so they hate the concept of the Jewish People. As in they hate Zionism.
The modern atheist tends to be violently against all religion and is typically ignorant of most religion and comes from a Christian background. They're culturally Christian and won't admit it. They'll claim they're secular but they'll still celebrate Christmas and see nothing wrong with stores being closed on Sunday. They'll be hateful if a Jew a doesn't celebrate Christmas and feels Saturday is the day of rest. They often don't get that Judaism is the culture of the Jewish people and that being Jewish is more than just a mere belief. They're also the kind of people to whine about circumcision and kosher slaughter when nobody is forcing them to get circumcised or eat kosher meat. They also tend to be 'anti-Zionists' but can't really explain the double standard they put on Israel.