Of course, that is usually the root cause of all forms of discrimination, in one way or another. DetlefK also breaks down some very specific reasons. Jews were/are always a small minority, and therefore an easy target. People seem to forget the Jews aren't a sizeable majority anywhere, except Israel. There are approximately 200 countries in the world, only two, Israel and the US, have populations over a million Jews (6.5K and 6-7K, respectively); only a handful have more than 100K, but less than a million; France, Canada, UK, Russia, Argentina, Germany and Australia. There are also a handful of countries which have no Jews. Jews make up less than one percent of the entire world population. This makes us a very easy target because there are so few of us, and there are those who won't/refuse to defend us.
There is also a tradition in Judaism which encourages education, so Jews are often seen as well (or overly) educated, and therefore "elitist" or as some like to call us "supremacists". This also stems from a misunderstood religious issue of Jews being "G-d's Chosen People". The "chosen" part has nothing to do with "being better than", but rather with "commanded" to follow His laws. But, even today, that is still bandied about as if it is "proof" of the concept of "Jewish supremacy". This is also is sometimes the basis of racist propaganda about Jewish involvement in ethnic minority rights. The white supremacists claim because the Jews see themselves as "better" than the "white man", they agitate and empower "lesser" (i.e. anyone not white) groups to rise up and challenge the white way of life, whatever that may be. Sadly, a slightly inversed version is used by ethnic minorities to claim the Jews are using them as "puppets" and therefore are even worse than "white men". If you read racist/bigoted literature, one will often see terms like, "the white man and the Jew are responsible for..." or "When whites and Jews...". Jews are almost always held out of the term "white man", except when the person is trying to paint the Jew as a "white supremacist".
Along with education, other tenets of Jewish law are cleanliness and eating habits. People in the Dark Ages and on saw this as "odd". Why the constant need to clean or bathe? Are the Jews a naturally dirty people? Well, that was the conclusion of some. Others, again, saw it as a form of elitism. But, when diseases would break out, it always seemed, to more than a few, that Jews were not affected or less affected than the population as a whole. This gave birth to Jews causing diseases, which led to the concept of Jews poisoning the water and food, but usually water. Blood libels were also born out of misunderstandings of our eating and food preparation habits.
As DetlefK said above in points two and three, the Jews were more or less forced into certain professions because they weren't allowed to be parts of others or own land. Banking was the one which cause the most consternation among people. It bore the "Jews are stingy/cheap.", "Jews only love money.", "Capitalism is a Jewish disease.", and all of that led to "Jews are the cause of most wars in the world." because, after all, it takes money to fund wars, and who held the purse strings? Jews! Who were agitators of social change (as discussed above)? Jews! This also leads to the concept that Jews are not a real minority in the sense they are oppressed, but rather then are a minority of oppressors, therefore attacking them is simply freeing oneself from their horrible yolk.
Really the question should be is why aren't more people willing to confront anti-Semitism? Why must anti-Semitism from the right or Nazis be condemned, usually with the condition of pointing out other groups are also the target, even when the attack is anti-Semitic in nature but ignored or even used by others? Anti-Semitism is a real problem. But, IMO, until it reaches near-Holocaust levels, most people don't give two shits.
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