Why has there been a conflict between indians traditions and some government programs since 1947?

Oof, too many reasons but lets start with the obvious.
The US Gov. didn't respect or view Native Americans as valid Americans or people of that land.
They limited their rights but enforced certain laws onto them. An example of this is where they didn't allow Native folks to vote but still made them pay taxes. This conflicts because taxes means that you are a resident/citizen of the land and so does voting.
They tried to limit their traditions by saying they were satanic.
The Gov. took their children and put them into schools where they could be reformed. This meant beating them if they spoke anything but english and cutting off their long hair (boys) which is a large traditional physical thing for Native Americans.