Israel has got to be a problem for any atheist out there. A country that has been formed around one religion with the express idea of having it as a safe place for all Jews to come to is one that should be almost ridiculous to anyone who has no faith or does not accepts religion dogma. Its almost like you would have “Pinocchio land” for all of those who believe in the story and want to live by it (praising whales, never burning wood furniture and so on).
On the other hand this country was formed as a result of mass genocide that has lasted for hundreds of years in almost any country around the world in one form or another, and which resulted in the systematic mass murder of the European Jewish population by the Nazis. Mass murder is not stranger to humans, it is believed that this kind of killing started with the dawn of man, and Jews are not the only ones who have been persecuted and killed, there were many other nations (that disappeared because of it) and many modern nations have been through this, however Jews are the only ones to have suffered a systematic, almost mechanic method of exterminating humans beings with the direct purpose to eliminate them and take advantage of anything the have or own. The state of Israel was established on the smoking ashes of millions of Jews and the global understanding that these people better have a country for themselves otherwise this thing could repeat itself.
Feeling hostility to Israel and what it stands for (Jewish state) is pretty normal from any atheist, but let us not forget the many Muslim states that have been there even before the Jewish state. These countries have not been established as a result of mass killing or persecution, but rather have been there as tribes who have evolved a sense of culture or common bloodline. And while Israel is a democracy that allows freedom of religion and expression, many Muslim states do not allow any new Churches or Synagogues built, and old ones can not be fixed or maintained, meaning that eventually there will be only Muslim masques.
Israel is a result of religious hatred and religious persecution over hundreds of years, it is a result of one nation that did not break even though it was exported out of its country and spread across half of the globe. Its people wanted to go back to their original land and practice their religion, as strange as it can sound to anyone who does not believe.