Answering as someone Jewish. . .

Jews don't assimilate (fully). In the Passover story, one of the things we note is that even living in Egypt for a long time, they didn't assimilate and they were disliked for it. Heck, how often do you hear people talking about other immigrants "not assimilating these days". For centuries, Jews even spoke a language other than the vernacular. We're a much more tolerant world today and yet there are plenty in this country (the US) that wish everyone "would just speak English". I have plenty of friends whose parents grew up speaking Yiddish in this country.

Likewise, Jews were seen as people with divided loyalties. But this, again, isn't specific to Jews. Kennedy took plenty of hits as people questioned if he'd "just do what the pope told him to do." Were Jews really going to be loyal to the state they lived in? In an era when wars were often fought with what makes today's reasons seem air-tight, would Jews decide to sit on the sidelines (since they weren't really X nationality)? I mean, imagine if the US and Canada got into a war over who could call they're syrup "maple syrup". Would you fight in that? People have fought for some stupid things. Also, during a decent period of time, mercantilism became a big factor in economic thinking. If Jews didn't see a problem with cross-border trade, that was doing economic harm.

For Christians, "you've heard the good news and yet you still reject Christ?!?" This is one of the more simplistic ones. People have killed (and continue to do so) for religious reasons. Jews were especially problematic for Christianity. Here you have the predecessor religion co-existing. If they thrive more than the Christians, does G-d like them better than the Christians? And there's plenty of "they killed Christ" to go around.

Jews are, in some ways, refugees. I mean, there was an ancient state that existed and then diaspora as the Jews had to leave their homeland. First, people often don't like immigrants. How much scapegoating happens even today around immigrants and crime, jobs, culture, etc.? Heck, even things like sexuality come into play. In a lot of anti-Semitic literature, Jews were portrayed as ultra-sexual in the same "hide your daughters" way that can happen with African Americans today. Second, people really don't like refugees. I mean, these are people coming with nothing. These aren't university trained computer programmers coming over like H1-B visa getters. These are people who have it really hard.

Beyond that, someone like Dawkins might point out that we try to propel our genes and like genes forward. A decent amount of history looks like people trying to force their culture, their nationality, and their genes forward through history. Jews were a different group. If you're under the impression that wealth cannot be created, then any wealth that Jews get is wealth that people like you don't have. So, it becomes competitive in that sense and people try to propel people like them forward through history.

I guess I'll also touch on the fact that diaspora Judaism somewhat flies in the face of nationalism. I mean, if you're big into patriotism and nationalism, then the state should be the citizen's first priority, right? I think a lot of us now see the state as a tool meant to make our lives more stable and just. We don't live for the glory of our country. Our country is meant to help us have better lives. When we serve our country, it's to enhance the lives of the people and increase justice, not to enhance the country (although they sometimes go hand in hand). This is a big shift in modern thought (at least to me). But diaspora Judaism can fly in the face of "commitment to your country should take precedence over commitment to something else". I mean, to us it might sound ridiculous to say that your country should matter more than your morality - and I mean secular morality here. But in a Europe coming out of feudalism where they were trying to define national loyalties and borders, worried about losing territory to the neighboring country, worried about all sorts of things that look foolish from a modern perspective, well, if Jews weren't going to care if they were Polish or Russian, that was a huge problem. Frankly, this is one of the reasons that Jews came to America. While America has its nationalism, it's pluralistic, and it's often based off good governance and democratic principles more than the history of most places.

Jews could also be insular. Kosher dietary laws meant that they didn't eat with non-Jews and that they bought their food from within the community. Again, it's easy to see how something like "those assholes won't buy meat from me saying my meat isn't clean!" turns into anti-semitism in the way rumors spread. Before cars, towns were organized for churches or shuls to be within walking distance which means segregation.

Heck, even looking at the Harvard example, you see a private club that had a certain culture that was losing that culture. No longer would Harvard be almost all Wasp. I mean, they and their forefathers had put their money and effort into it. Shouldn't their progeny and the progeny of their religion and culture get the benefits of it? I'm not saying you should agree with that logic, but it is logic that is often used. I mean, there are people who don't want this country to become Spanish speaking or bi-lingual. Whether someone is the first person someplace or not, people and culture become entrenched and people don't want to see that culture change away from them. Heck, how much complaining do some people do that a lot of advertisements don't say "Merry Christmas"? Harvard was created by Wasps and now it was benefitting Jews and turning more Jewish. The identity of the institution was changing.

It isn't that the hatred is that different from a lot of other ethnic hatred. A lot of it can be seen in a lot of the other ethno-religious hatred that has existed in the world. It's that the Jews hit a lot of different sore points in human history. There was religion, there was national identity, there was immigrant status, there was language, there was hope of another homeland, their was separateness/insular-ness, etc.

I come from the point of view that nationalism is a bit outdated. People deserve to be justly governed in ways that make their lives better and that they should be allowed to choose how to live their lives in a way that makes them happy (clearly with restrictions on things that cannot be abided like murder). But providing good, just governance isn't why Europe has so many countries. Good governance and happy lives for citizens isn't why England subjugated Wales. Justice isn't what drove the Reconquista of Spain. Power, control, and the perpetuation of one's genes, culture, language, and religion have been a driving force in human history.

I, for one, am happy that we at least see such injustice and hatred as a bad thing these days. I'm not sure if you were looking for an answer like this. I didn't mean for it to be long like this. Hatred can be a bit hard to wrap one's head around (at least for me) and yet it's defined a lot of human history. I can't imagine someone hating me without knowing me. I don't understand it. I'm nice (honest)! Yet, even without understanding it, I know there are people who wish I didn't exist who don't even know me. It's actually quite an odd feeling.