Extreme forms of Antisemitism existed long before even Muhammad was born. You are probably referring to the outcome of a half a century long conflict. Yes there is a lot of anti-Jew factor in the Muslim world(I am a Muslim my self).
But there is also a lot of anti-Muslim factor widely prevalent in the west too! Every bit of people on this earth have suffered with that problem. The Muslim world looks at these problems from their own view. Think of it this way, there was no signs of Israel in the Arab world around a century back, the settlements start. There are splinter groups. Slowly albeit steadily a vast majority of the native population was displaced to settle new set of people. A new nation is declared, backed by most powerful nations on earth. What was your country yesterday is not today and you are mercilessly kicked out. Now what sins did the natives do to deserve that? On top of loosing their lands, there is huge under development and humiliation since decades. How do you expect them to react?
To quote Ben Gurion himself:
I don't understand your optimism. Why should the Arabs make peace? If I were an Arab leader I would never make terms with Israel. That is natural: we have taken their country. Sure, God promised it to us, but what does that matter to them? Our God is not theirs. We come from Israel, it's true, but two thousand years ago, and what is that to them? There has been antisemitism, the Nazis, Hitler, Auschwitz, but was that their fault? They only see one thing: we have come here and stolen their country. Why should they accept that? They may perhaps forget in one or two generations' time, but for the moment there is no chance. So, it's simple: we have to stay strong and maintain a powerful army. Our whole policy is there. Otherwise the Arabs will wipe us out.
- http://en.wikiquote.org/wiki/David_Ben-Gurion
Tomorrow if some state like California is invaded by some one, existing citizens of the state thrown out. How will those people react. Will they laughingly walk out of their homes, stay in tents and welcome the invaders with Garlands? And business goes around normal?
There isn't a community on earth today which is different than any other community. People everywhere are just the same. When these sort of things happen friction is but natural but to take place.
All nations and their people on earth or same, Jews, Muslims and Christians. No one is different. Now there is also a clash of cultures. Others like their culture as much as you like yours. To assume everybody must follow your way of life is unacceptable to any community on earth.
I come from a nation(India) which hasn't attacked/invaded any country in thousands of years. We even got our freedom through complete non-violence. For thousands of years we absorbed other religions, cultures and languages and their people with open arms. Tolerance is not everybody's cup of tea.
Friction will remain, the way out is tolerance and respect for others.