The land mass of the U.S. was essentially empty when the settlers arrived. The fact that a few million (or less) aboriginals eked out a primitive existence on the land prior to that is not relevant to the debate of "who owns the land". Those questions were settled by our ancestors, maybe not to the liking of everyone, but you can't please all the world.
From about 1515 to 1648 most of the Americas were subjected to enormous and deadly plagues.
If you've ever looked over Jamestown's history you would have noticed that about 90% of the first 60,000 "settlers" died of disease within a few months of their arrival. Definitely some problems here.