What were the longer term more fundamental causes of the inability of whites and indians to avoid such events as the wounded knee massacre?

There was a greed for land and the whites wanted the Indians off the land. The Indians on the other hand, wanted to retain the land that had always been there. As the Indians were forced off their lands into reservations many of the promises (treaties) made by the whites were not carried out or honored. As the Indians became more and more marginalized they fought back which lead to massacres like the one at wounded Knee SD. It all comes down to a battle for territory, sadly.