Warning- the following is posted by a Jewish atheist:
It is complicated as far as I can guess. Several things, including some mentioned above, come to my mind:
1. Being of a different religion yet living as a minority (post diaspora) within other cultures for many, many years. Therefore Jews suffered all of the suspicion directed at any minority, particularly religious minorities, while in the very societal and geographic heart of another, majority religion. Makes for a lot of paranoia! And of course religious divisions are among the most emotional and generate the most savage responses.
2. Add to that the fact that Jews had to either retain their own distinct forms of dress, food requirements, social rituals or assimilate within the larger culture to some extent. The former were often considered weird alien others; the latter were considered to be sneaky potential conspirators who were only pretending to be part of the larger culture for some nefarious purpose (probably so as to have sex with the majority women. as is attributed to any minority).
3. Being portrayed as "killing Christ" certainly didn't/doesn't help how Christians view Jews.
4. As noted up thread, Jews have often be restricted to/allowed to do jobs that the larger majority was not permitted to do. Not infrequently this was an intentional method by the leaders of a society to further divide Jews from the rest and make them more unpopular.
5. What is particularly resented in a minority is success, and Jews have generally been seen as somewhat more successful in a number of fields than the average population. Although I have some relatives who would like to attribute this to something special about Jewish genes (who doesn't want to feel special simply from being born, right?) it seems clear to me and to most of the rest of my relatives that if there is a difference, it relates to a long-held emphasis and appreciation in Judaism on education. Look at the fields in which Jews are thought to be more represented than in the overall population- typically they are fields that are linked to higher forms of education.
BTW: I see a very similar resentment of Asians in non-Asian cultures for much the same reason- their economic, academic, artistic, and musical success which arises from pretty much the same basis- an emphasis on education (and on family). And like Jews, Asians have distinct cultural rituals, many have distinct religions, etc. They are "different" from the majority in certain societies (although not in the world as a whole), and different often creates dislike.
6. I should note that I start to feel uncomfortable when even well meaning people are incautious with their attributions of some of the stereotypes. Even positive ones. Such as the ideas that Jews are typically wealthy, or insular, or haughty. The vast majority of Jews I know are middle class. No international bankers in my group of acquaintances! A Rothschild would spit at me if I could ever find one. My father and I buy stocks and stuff high and sell low- we have no ability with money whatsoever! I, my family, and friends grew up as typical Americans- went to the same schools, watched the same TV programs, read the same comic books, thought the same thoughts, and even ate the same foods (minus the ham) as any one else in America. We identify as Americans first and foremost, not as Jews. We are Americans who happen to be Jewish in the same way some Americans happen to be Catholic. Perhaps with a little mix of the idea that we are Americans with a Jewish origin in the same way there are Americans with an Italian origin (because of the intertwining of Jewish being both a religion and often an ethnicity).
I am often surprised when a non-Jewish American assumes that I am somehow different from them. Or that I have a different loyalty than they do. Hey- I am a typical baby-boom guy- and I love my country, the USA, just like anyone else. I have no more loyalty to Israel than to Sweden. Sure I like knishes and corned beef sandwiches, but so do many Swedish-Americans. And I like Ikea meatballs too. So the very nature of these discussions, which inevitably stray into how Jews are "different" can often be disturbing to me. I don't feel different. It is very strange when I find that there are people who think that I am different, and hate me for it. I can accept being hated because I am an American, but not because I am Jewish in terms of my cultural background.