How did martin luther's publication of his 95 theses affect european understanding of government?

Luther began the Protestant Reformation, and the Catholic Church had its own Counter Reformation led by St. Ignatius of Loyola. He also founded the Jesuits, who vow personal loyalty to the pope and are primarily a religious order. 

The Jesuits were important missionaries in French and Spanish America. One of the most important explorers of the Mississippi River Valley was Father Marquette, founder of a mission in what was to become Chicago. 

Many of the early settlers of England's colonies in America came for religious regions. Among them were the people called the Pilgrims, who had fled from the persecutions sanctioned by James I. James I was a Protestant (Church of England) but the Pilgrims (and later Puritans) didn't think he had gone far enough. 

Luther's challenge to the Church led to the Thirty Years' War. The Thirty Years' War (1618–1648) was a religious war principally fought in Germany, where it involved most of the European powers. The conflict began between Protestants and Catholics in the Holy Roman Empire, but gradually developed into a general, political war involving most of Europe. The Thirty Years' War was a continuation of the Bourbon-Habsburg rivalry for European political pre-eminence, and in turn led to further warfare between France and the Habsburg powers.