The two differed in terms of: A. Way of earning salvation B. Its organization C. Belief of papacy and sacraments D. Bible

Early in the time of the Reformation, Protestantism was relatively monolithic.  There were some sects with some differences even early on, but those differences were much less pronounced than they are today.  Therefore, we can identify some differences between Catholicism and the great majority of Protestants at the time.  These differences included:

Church hierarchy.  The Catholic Church was very hierarchical.  The Protestants did not think there was any reason to maintain a firm hierarchy.  They wanted more autonomy for clergy and for individuals. 

Salvation.  One reason why they wanted more autonomy was the fact that they did not think that “works” could earn salvation.  In the Catholic Church at the time, a person won salvation by doing the right things.  Going to church, taking the sacraments, even buying indulgences helped to earn salvation.  The Protestants believed that salvation came through faith alone, not through works.

Bible.  Relatedly, the Protestants were much more Bible-centric than the Catholic Church.  The Catholic Church held that Church teachings and traditions were as important as the Bible.  It also held that people needed the Bible explained to them by priests.  The Protestants wanted people to read the Bible for themselves so as to build a more personal faith.