moghrabi: I do think there is a difference between "Jewish Israelis have more opportunities (rights) because they are of the Jewish religion/nation" and "Israel is a country for Jews only". This might sound vague so I'll explain:
Now, as pointed out in your article, there seem to be several occasions in which Jews have an advantage (more rights) than non-Jews: the Law of Return, the IDF-question, etc. I do not think that is just. To explain it is another thing though: according to the Zionist doctrine, every Jew on the planet can (and preferably should) view Israel as their homeland. If a Jew immigrates to Israel, it is seen as someone "returning" to his homeland (that's why: Law of Return). This is not so much of line with the way how other democracies handle this; Russian Germans - for example - can "return" to Germany in the same sort of regulation (although the majority only speaks Russian). In Israel, there are indeed other rules concerning the immigration of non-Jews, requirements which aren't required for Jewish immigrants. This is in one line with the requirement of Israeli citizenship: Jewish immigrants get Israeli citizenship instantly; non-Jewish immigrants have to wait a couple of years before they are granted the same citizenship.
After that has happened, it still depends whether all Israelis have the same rights, as seen with the IDF-question. Than there is the rabbi leadership which still regulates matters like marriage - which is however, not in contrast with a certain amount of other democracies (not that I agree with it, as I am a supporter of a secular state, where church and state are divided) and countries.
These examples however still do not match with "Israel is for Jews only". Non-Jews are accepted in Israeli society (I guess especially Christians that is); and in a country where the majority of its citizens are Jewish, that will be the dominant tone in rule.
Now, I understand that some things are seriously wrong. e.g. The Law Of Return is indeed solely based on those who are Jewish. I find it highly unlikely that these things will change; as Israel is indeed the Jewish State (as Germany is the German State, or Ireland is the Irish State), they want the Jews in the diaspora to keep emigrating to Israel.
What I would say is the following: not "Israel is for Jews only", but: "Israel focuses on (diaspora) Jews as their citizens, but do not object to non-Jews living inside its borders".