You might want to look at Charles Mann's account in 1491. Chapter 2 'Why Billington Survived' is what I'm basing this response off of. You can't really think of it in terms of Native Americans as a whole. There was a specific group (the Wampanoag) who had just suffered a terrible epidemic. This put them at a terrible disadvantage against some of their surrounding enemies. Massasoit (the leader of the Wampanoag) and Tisquantum (who had originally lived at the place the Pilgrims called Plymouth) both hoped to ally with them for their own gain. Massasoit was hoping they'd help in fighting against the Narraganset. Tisquantum was hoping to rival Massasoit for power. It wasn't so much the guns that Massasoit was after. He probably was trying to exploit the fact that the Narraganset were trading with the English. If he could convince the English to fight the Narraganset, that would probably cause issues for their trade relationship. At least, that's what Mann suggests.

tl;dr - An epidemic caused a crisis with a specific group of people who thought they could exploit the newcomers to their own ends.