The three primary reasons the Indians lost to the whites are, in order of importance:

1) Lack of adequate immune systems (#1 by a long shot).

2) Failure to see it as a "white civilization vs. red civilization" conflict and instead view each individual battle as a tribe vs. tribe conflict.

3) Marginally inferior military tech.  Horses and canon were a massive advantage for the Euros, flintlock and matchlocks were equally or less effective than most Native bows.

But Ken is a Kon and all he can fathom is guns and how awesome they are so there you have it.