Although he is a Christian now, President Obama dabbled in Islam as a teenager. Of course he is going to have more sympathy for Arabs and Muslims, and rightfully so. Keep in mind, the state of Israel didn't exist until the United Nations stepped in after World War II to create a Jewish homeland. The move usurped Palestinians and Muslims already living in the area, so of course those people are going to be upset. Israel, despite Hitler's genocide, has no right to exist in the first place because the UN unfairly displaced residents already living in the Holy Land. Obama isn't necessarily siding with Arabs and Muslims, he is simply more acquainted with the facts than some of his conservative predecessors (i.e. the Bush family and Reagan).
I don't it is safe to assume that Obama has more empathy towards Arab and Muslims than Israelis because Israel is all ready a developed nation. Yes, all of these countries have oil, but Muslim nations are lacking administration. Obama is looking at this as the equal administration oppertunity for all the middle east nations that why Obama is considering Muslims and Arabs problem.