The issue of authority was the other great controversy during the Reformation. Besides justification by faith, the authority of Scripture came to the forefront and rightfully so. Today this is known as sola scriptura, one of the five solas.
This issue became so prominent for Martin Luther and others as the traditions of the Roman Catholic church at the time (and now) for justification were rooted in penance and merit and works. Scripture teaches none of the methods as a way to salvation, only justification by faith. Rome set these traditions as equal to Scriptural authority.
Mark 7:9 tells us that we are not to observe the traditions of men should they make us disobey Scripture. And so, Protestantism, the Reformed, holds to sola scriptura. Yes, we embrace creeds and confessions but the bible will always take precedence in any conflict especially in conflicts with traditions of men. Scripture is and always will be our highest authority.
An outstanding explication of sola scriptura can be found in the video below by Mark Driscoll of Mars Hill Church in Seattle.