So to repurpose this answer a bit:

Jews were a minority group that was tiny, but present in a wide range of European societies. Sadly, minority groups are often subject to mistreatment and exploitation. Being a minority in a lot of places makes it rather likely that that group will often be subject to bigotry.

Anyway, in Europe different ideologies/goals often aligned to make persecution of Jews a favorable outcome for different levels of society. For the nobility, getting rid of the Jews meant getting rid of their debts to Jews. For kings, Jews were a handy source of income if you wanted to levy a "I want money and Jews have money" tax. For all members of society, there were religious reasons to oppress Jews, which could be exploited for the above means, but also could be its own end.

There were also historical causes for it, even then. Since Roman times, Jews had been treated legally as a special legal entity. This meant that Jews were not, generally speaking, considered normal members of societies they lived in. They were a social and legal category all their own, generally operating under a royal charter, which set the legal terms of Jewish residency in a place. This meant that Jewish communities were directly controlled by the king, with no nobility to counterbalance. That situation made is relatively easy for kings to pursue the above persecution reasons--there weren't legal or social issues involved in persecuting Jews. The only thing preventing persecution of Jews was local governmental authorities not wanting there to be persecution of Jews, which for the above reasons was not always the case.

This is an extremely broad question that has no one answer. It's like asking when racism began as a concept, but we then must address the historiography of racism and what racism meant to different cultures in different time periods.

Modern anti-semitism typically emphasizes the ethnic cleansing of all Jews in a certain nation. This is different from the anti-semitism of Ferdinand and Isabella's Spain, which was a massive push towards conversion that had its roots in an ethnically "pure" Spain that became an obsession in the centuries following the Muslim Expulsion. There are as many examples of anti-Semitism throughout history as there are examples of fear or hatred towards any ethnic group.