No, it's just a widely accepted term for descendents of the people who inhabited the Americas before European colonization. Their (long ago) ancestors are also our long ago ancestors in Africa.

The reason "indigenous" is used is mainly historical, but there aren't any better modern terms. "American Indian" is largely a US term and one a lot of people don't like. "Native American" has similar issues. "First nations" is mainly used by Canadians and doesn't encompass all the groups being discussed. "Indian" works, but "indigenous" has a lot less semantic baggage.