Mainly they've always been forced to immigrate to new areas due to being expelled multiple times from what is now Israel. Therefore, they've been considered invaders of sorts, similar to how people in the US view Mexican immigrants. Of course Arabs have a deeper hatred as they believe that the Jews usurped their holy land. Anyway, the article doesn't directly speak to the reason for their perseuction, but you can read between the lines.
However, that Jews have serious problems with integrating due to their unique culture and religion is one thing, but another thing one might remember, is how they traditionally administrate their money as family fortunes.
We have a situation here in Europe now where immigrants from the Middle East are using the same administrative family-fortune system as the Jews have throughout history. The Middle East immigrants basically run all the smaller shops in northern Europe now. They have huge closed networks, and you often see them driving around in very expensive cars (but they are rarely owned by the individual behind the steering wheel, but by the entire family). As a result, they are often accused of being criminals and hustlers.
I believe, that the Jewish(/Arab) family-fortune system, and their closed networks, are one of the things that have made them haunted through recent history. Right now, the third largest political party in Denmark, is one that basically wants to see all the immigrants to the door as soon as possible, and they have already successfully made it very hard to immigrate to Denmark.
History repeats itself, but now in a more civilized manner.
I basically believe this to be a clash between socialism and older traditions, as you don't need a strong family to prevail and retire economically in Europe anymore. But that's a seperate post.