Apartheid? No. Bad? Yes.
One of the big problems with the State of Israel is that because Israel itself has no history of systematic racial segregation, they aren't nearly as sensitive to discrimination when it does happen. To use a metaphor, imagine racial discrimination as a disease. The United States had a rather severe case about sixty years ago, and as a result, we are now more sensitive to it. Have we purged racism from our society? No. But we do try very hard to shut it down. Israel, on the other hand, lacks that history. And while you'd think that being subject to so much discrimination throughout history would make Jews sensitive, it's not so easy to recognize it when you're the perpetrator.