How has the Protestant reformation influenced how we in America today view freedom, government, and rights?

One thing you should be aware of, when speaking about the Protestant Reformation, is the degree to which it was deeply destabilizing throughout Europe. Religious Wars, sectarian violence, religious suppression—these are all key themes concerning the Reformation's impact on Early Modern Europe.
If you look at the history of English colonization, consider that a significant number of colonies were founded by religious minorities: for example, consider the Puritan presence in New England. Then there is a place like Pennsylvania, founded by the Quakers, or Maryland, by Catholics. Even as far back as the colonial era, you can observe a significant amount of religious diversity in Colonial America.
Now we come back to the founding of the United States itself, influenced as it was by Enlightenment era criticisms, and by the history of religious tensions and religious suppression that was deeply threaded in European history. Religious liberty was one of the key guarantees of the First Amendment (and this was particularly important, precisely because of the history that could be observed back in Europe). Meanwhile, one has the lasting influence of Thomas Jefferson and his ideas concerning "the separation of Church and State." These values have served as cornerstones of American democracy all the way through to the present day.