People who came later however, were not so understanding and also tribes in other areas were more warlike.
The combination of settlers who were less tolerant plus the more warlike tribes, such as the mohawk, and the mother of all eastern tribes, the Deleware, and all the other eastern and north eastern tribes, and the fact that the British and the French used various tribes in their wars against each other was not condusive to the survival of the native Indians.
Down through history more advanced civilizations have absorbed or wiped out less advanced civilizations. It isn't the ideal situation but it is the way it was. Crying and moaning about it now will not change things.
Making the pilgrims, the least offensive of the people who came to these shores, is ridiculous and this tribe in SF that did this is showing their prejudice and lack of understanding of the way things really happened.
After that time the Indians had to make deals with the Europeans since they could no longer mount a serious military presence.
It's worth noting that the war between the Iriquois and Mohican Indians that had been going on for 300+ years ENDED due to the absence of Mohican warriors. They were adopted by the Oneida. You can find them today at lake Winebago ~ they are the Munsee Band.
Disease did the job.