How were the goals of Charles and the Holy Roman Empire at odds with the desires of Lutheran princes?

The goal of the Holy Roman Empire is to keep the unity of it's territory thru religion. But many rulers of Germany supported Protestantism. They did not like the authority imposed to them by the Pope. The Holy Roman Empire, under the rule of King Charles V, created the Couhter Reformation, in order to convince people to go back to Catholicism. Unfortunately, Counter Reformation was not able to succeed, thus, forced the Holy Roman Empire to seek peace with the Lutheran princes. The Ausburg settlement was the dign that the religious struggle has come to an end.