I think deep down it is that people are afraid of what they do not understand or know. I've met people who have never met a jewish person, and he actually asked me if jewish people have horns(I live in an area where there is a big population of jewish people. My school is 70% jewish. So apparently to them I was an expert on it). Of course I said No. But it just shows what ignorance does.
I think deep down they were just an easy target from time to time. Seriously, after Masada the next great Jewish revolt has got to be in 1944.
Talk to my dad, his mom was shot and his aunt killed during the occupation. I think he may disagree with your thought that the Palestinian's land occupation is BS. But he doesn't "hate" Jews, he is just opposed to the idea of Israel, and everyone is equally entitled to their opinions.