What in Smith's letter might offend non-Mormon Americans?

There were many reasons. For starters, he wished for a New Jerusalem, or Zion, to be built on the American continent, implying that it would be a country governed by religious beliefs and as many were not mormons, they disliked it. In addition, he claimed that the Native Americans were descended from Israelites, which also implies that the American expansion based on beliefs that they're savages and beasts is fundamentally incorrect since the Natives were just as human as the colonists. There were many more reasons.