Many Protestants believe that their own Christian tradition is not related to the Catholic tradition, but in fact stems directly from the time of Jesus. The Baptists, for example, often say that theirs is the true line of Christian thought that can trace its way all the way back to John the Baptist. They see the Catholics as an extreme perversion of the true Christian tradition, and claim to not have any shared roots (beyond of course the earliest years of Christianity with the Catholic Church).
This is not the case. Many Protestant traditions (Christmas is an obvious example, infant baptism, stained glass windows, etc.) stem directly from traditions that originated among Catholics. Much of the theology of Protestantism, in fact, also stems from the Catholic tradition. In some of the Protestant traditions many of the creeds which still make up the essence of the faith were originally Catholic creeds.
Despite shared history and traditions, there is still a great amount of difference between Protestants and Roman Catholics. Perhaps most obvious and the best well known is the fact that Protestants do not hold allegiance to the Pope. They do not see the Pope as any sort of special office, and do not recognize the authority of the Pope over their spiritual lives.
Many Protestant traditions also lack the bishoprics and clerical hiearchy that exist among Catholics. This is not to say that all Protestant traditions lack this. Lutherans, Anglicans, Episcopalians all have clerical hierarchies that are very similar to those of Roman Catholics, although excepting of course the Pope as the head.
Protestants also reject the idea of praying to saints. Many Catholics hold the reverence of saints very dear to their faith, and it has become an integral part of the Roman Catholic religion. Praying to saints for intercession, praying to the holy Virgin Mary, these are items that are vital to Roman Catholics but which are not highly regarded among Protestants if not outright abhorred.
It was in fact this reverence of saints that made up some of the strongest problems that the Reformers and Protestants had in the 16th century when first they began to separate from the Roman Catholic Church. They referred to Catholics as idolaters, among the other ills and sins which they heaped upon followers of the Roman Catholics Church.
The earliest decades and even centuries of the split between the Roman Catholic Church and the newly formed Protestant and Reformed traditions were extremely violent and chaotic. A prime example of this is one of the important founders of the Calvinist faith, Ulrich Zwingli. An important theologian Zwingli also became a warrior fighting against the Catholic Church. It is said that he died in battle, a bloody battle axe in his hands.
But to think that these are two completely separate institutions is incorrect. There are many differences between Protestants and Roman Catholics, obviously, but there are also many similarities and a strong shared tradition dating back well over a millennium.