Both South Africa and Israel were created by European refugees fleeing persecution. Both countries became very militaristic and has Western allies who overlooked the way they treated their natives. Both countries where populated by a people who felt that their culture was under attack and vulnerable.
No one is overlooking the way Israel treats the natives. They treat the Jews fine! Oh, by natives you meant Arabs? Well that would just be a fallacy to say that.
In South Africa, the minority ruled OVER the majority. THAT is the definition of apartheid. In Israel, the Majority rules the minority. Which is the definition of democracy.
Also, there is a reason they are called "Arabs" and not "Israeli", its because they are originally from Arabia, not Israel. They have no roots in Israel.