Well, largely because the Arab countries are not. They do bad things, yes. They did a one-time expulsion of Jews, which is now no longer on going. They have highly discriminatory immigration policies. They have abusive "guest worker" programs that end up as de-facto slavery for many. These are pretty bad things (though discriminatory immigration policies is pretty uniform, the world over), but these things are not generally what people mean by apartheid.
It's not fully fair to describe Israel as apartheid either. Its actual citizens largely have the same rights on paper no matter ethnicity or religion (though the religious marriage laws are an oddity, and the inability to intermarry does make it comparable to those prohibiting interracial marriage in South Africa).
But it is actually somewhat fair to compare Israel to apartheid South Africa. They have an active, ongoing separation of populations into segregated areas and even nominally independent states, that have no effective autonomy due to the overwhelming power and actual physical control of Israel. The Gaza strip and the West Bank are nearly direct equivalents of South Africa's bantustans. If you accept that Israel does have real sovereignty over all the territory it occupies, the differences in how it treats different people really don't seem just.