I believe it is a myth that Israel is one of our closest allies. Certainly, the Holocaust produced sympathy for Jews in general, and, because of this horror, Israel has been viewed as the "only" victim in various Arab/ Israeli conflicts. Jews, as a group, were victims in Europe, and Islamic countries were not responsible. Mohammed's comments on the People of the Book, during his "Night Visit" to Jerusalem gave Jews more protection in the Islamic world than they received in Europe until the advent of modern Israel. As people of the book, Christians have been part of Islamic governments, including Saddam Hussein's. Various Arab/Israeli conflicts have limited Jewish participation in Middle Eastern governments.
The US has never gone to war in the Middle East with Israel as an ally. Before any war in the area, American governments always touch base with Saudi Arabia, with whom we have had a relationship since well before modern Israel existed.
The US, for all its failings, is a multireligious and multiethnic state, and a close relationship with a nation that favors one religion or ethnic group over another religion or ethnic group is unnatural.