Natives were excluded from the political system, just like they are in Israel.

Natives were seen as savage threats to colonists. In Israel, Palestinians are seen as terroristic threats to settlers.

They're very similar and the main differences are eras, technology, and geography.

America is a lot larger and at the time the surveillance and military technology didn't exist to round every native up and put them in an open air prison. Where there were large communities of native Americans living in organized settlements, the government ran largely the same playbook Israel does today: move them from preferred areas to areas nobody wanted, put them in camps when camps existed, go to war with them directly, etc.