At first the Native Americans thought the Europeans were welcomed guests. Soon however the Natives realized that they were intruders meant to take their land and resources. The Europeans infected the natives with disease. Hundreds of thousands of natives died as a result of these diseases. The Europeans and Natives in almost every encounter started out as friends but ended up enemies.
In short, the Natives didn't understand the Europeans. They learned of Christianity, and the lessons that go with the religion. But they didn't understand the people, that on one hand spoke of love, while the other hand was raping, murdering natives and stealing their land.
Native Americans saw the Europeans as god like since they were introduced to new items such as ships, weapons, metal, clothing, and other accessories which they never came across before. Many native peoples from all over the world have welcomed foreigners and were curious to meet them, but as soon as they can see the real motive of these explorers then the natives will want to push them off their land.