Yes, Jews are native to the Middle East, specifically the area of Israel/Palestine. But why should that make Palestinians who lost their land feel any better? It's irrelevant.
It shouldn't, and it doesn't. I agree that it doesn't and that Israel's treatment of Palestinians is terrible. My point is we can have this discussion without also (incorrectly) relying on anti-Semitic tropes of Jewish replacement.
(I am Jewish, but I do not support the Israeli government's treatment of Palestinians.)