That's fine. It's true that Jews have been living in Palestine for thousands of years. Those Jews obviously have every right to continue living there.
But Zionism is a European Jewish colonialist project. And it's this, not the fact that Jews live in Palestine, that people take issue with.
The fundamental flaw here is the idea that because SOME Jews have lived somewhere for a thousand years, ALL Jews have the eternal right to come there and displace the native population.