Well, some of those people obviously want to disassociate themselves with the state of Israel. They're not necessarily self-haters but they're definitely Israel-haters.
In all fairness, I don't think that all of the people who want a separate flag for the "Jewish" identity than the "Israeli" identity are doing it because they hate Israel. They probably just think that it's not appropriate to have an Israeli flag to represent them as Jewish because they're not Israelis and they don't consider themselves as Israelis.