My guess is that anti-Semitism, outside the Middle East, which is, I agree, a territorial problem, ebbs and flows with good times and bad. One reason it grabbed hold successfully in Nazi Germany was that there were so many economic problems and a handy scapegoat was available. As our economy and those of other countries deteriorate, I think anti-Semitism is on the rise.
However, I also think we are evolutionarily primed to fear or dislike "the other," which has allowed us, over the years, to make instinctual "decisions," fighting or fleeing. This instinct does make for some bad choices, obviously, being both under and over-inclusive, but if we cannot generalize in some ways, we have no way of getting through our lives effectively.
This "other" response is by no means limited to Judaism, as evidenced by the attack on the Sikh temple, the recent attempts to bar Islam mosques in various sections of the country, or the treatment of Christians in Islam-majority countries.
The fact is, though, that in order to have a sense of community, we have a need to separate ourselves from others in some way, and we need a way of recognizing who is a part of our "tribe." That means that one religion must distinguish itself from others. Judaism in its earliest days, took great care to be very different from the "religions" that surrounded it, as did Christianity, which carefully separated itself from Judaism.
Will we ever evolve to a point where none of this matters? Will our higher brains manage to always overcome the more primitive parts of our brains? Not in my lifetime.