Israel is not perfect. Far from it. Israel has some very serious problems, with its internal politics, as well as with its relations with the Palestinians. That statement is so obvious that it's almost ridiculous to have to say it, but I never want to be accused of being in the “Israel can do no wrong” camp. Israel can do wrong, and it has. And it's the right of anyone, Jewish or not, to criticize Israel when it does so.
But, when that criticism become so ridiculous, so disproportionate, so completely disconnected from reality, we have to ask ourselves about the motivation for that criticism. Is it an honest concern for the country, or for those who are being wronged by the country? Or, is it an attempt to demonize that country, and cut off any reasonable debate?
So then, why is Israel called apartheid state? Because by comparing the freest, most equitable country in the Middle East to the former South Africa those who hate Israel hope they can persuade uninformed people that Israel doesn't deserve to exist just as apartheid South Africa didn't deserve to exist
Imagine, for moment, that you do something wrong. Something serious, but not egregious. And then I call you on it—I point out what you did wrong, and hold you to account for it. We can disagree on whether or not you did it. We can disagree on whether or not you are wrong. We can disagree on how bad it was. All reasonable.
But then, imagine instead that I just begin the conversation by calling you, in all seriousness, an evil, worthless scumbag who deserves a painful death. Would you consider that to be, in any way, a reasonable approach? Would you try to engage me in a rational conversation, explaining that, in fact, you are not an evil worthless scumbag? Or would you assume that I was crazy, unreasonable, and/or just out to get you?
When someone calls Israel and Apartheid state, they aren't engaging in reasonable discussion. They're screaming at the top of their lungs that Israel is evil, and they don't want you to think, and they don't want to listen.