Kudos to @thomasPornin for a decent outline, but I think the answer is broader than that.
As I said above, I think the answer is that the Jews do not merit the abuse they've suffered, but I think it may be helpful to outline a few more answers.
The alien among us. As Mr. Pornin says, Jews have traditionally followed customs that set themselves apart from their neighbors. I will not try to explain why, but I will observe that humanity has a visceral hatred for people who refuse to conform to local norms. Because Jews obstinately continued to be Jews rather than fully assimilating, they have been subject to abuse on the grounds that anything different from us must be brought into conformance with us. If they don't assimilate, then they must think they are better than we are, and the only response to such behavior is to destroy them.
Aliens cause misery - the above problem becomes worse if the community has any bad luck. Humans blame bad luck on those who are different, and on those who cannot retaliate. From witch burning to pogrom, it is obvious to humanity that the cause of all misfortune is aliens living among us.
Poles live in Poland, Germans in Germany, English people live in England.... I still hear this one today; an acquaintance of mine said this year with a completely straight face that it was utterly unreasonable and wrong that Jews and Gypsy's [his term] argued for toleration. Everyone should just live comfortably among their community and the fact that Jews and the Romany don't have a country make them annoying, and that in order to stop annoying him they should stop being Jews and Rom. Obviously his sense of order in the universe is far more important than their identity. This fell into the category of idiocy that was too large for me to confront that day, but it is another source of hostility. (We will ignore concepts such as Welshmen living in the United Kingdom or Cornishmen living in Britain, or even 500 years of history of Englishmen of African descent. We'll also ignore the notion that "Germany" is a modern concept. ) This level of stupid is not going to be convinced by logic or reason. (this is also the ostensible reason why National Socialism/Fascism has such difficulty dealing with Jews; the underlying ideology says that individuality should be suppressed in favor of a national identity, and cannot deal with internal diversity. Obligatory disclaimer - I'm trying to explain an ideology that is stupid beyond my ability to comprehend; please don't assume that I agree with the thought or the consequences).
As I said, the reasons arise from sociology, psychology, and the fundamental hopeless stupidity of homo sapiens. Although it is a problem with historical consequences, it cannot be understood through historical analysis.
The first answer to your question (and the only responsible answer is "nothing; the Jews don't deserve the hatred). The second level is from that noted philosopher Kay, "A person is smart. People are dumb, panicky dangerous animals . . . . " The third answer at a more detailed level is book length, and I suspect, still inadequate.