It's not her hatred of Israel that many people upset, but the anti-Semitic implications of her words. People are allowed to criticize Israel - trust me, it's not all that uncommon - but parroting talking points used by outspoken bigots isn't something that people are as willing to tolerate. What she said, or at least the implications of what she said, don't amount to simple "criticism".
If you want to ask about how isn't allowed to be criticized, I'll point you to certain people who go out of their way to shut down any criticism of Omar's comments. Some people don't tolerate that one bit, often citing some aspect of her background (black hijabi-Muslim refugee woman). Fortunately a lot of people do tolerate criticism of Omar, specifically focusing on her individual actions, but there are a noticeable amount of people who don't. Furthermore, if you want criticism (or quite frequently, "criticism") of Israel or the so-called "chosenites", just go into a many a university lecture hall or a far-right rally. A lot of people left and right, particularly away from the center, will happily oblige you, since they're allowed to "criticize" Israel (where others more readily counter blatant hate).