The immediate effect of the Protestant Reformation was to create a new division within Europe, one which had both a religious and a political basis. Europe had always had divisions, before and during the Christian era. Considered from the standpoint of the continual wars and invasions, the dream of a unified continent had never been achieved. The closest situation to this occurred before the adoption of Christianity during the so-called Pax Romana, usually defined as lasting from 27 BCE, the start of Augustus's reign, to 180 CE, the death of Marcus Aurelius. From this point, internal divisions within the Empire, the long period of invasions, and finally the attempts to reorganize Europe politically in the centuries after the Empire fell all led to a state of continued instability and warfare.
In the sixteenth century the Protestant Reformation resulted in the split of Europe into an unprecedented two entities and a succession of new wars that now had religion as their rationale. The Peace of Augsburg in 1555 was supposed to represent a stabilization along the lines of the status quo of Protestant and Roman Catholic territories, but it was only a temporary peace. The Protestants themselves became factionalized into various sects or denominations. The English secession from the Roman Catholic church was originally separate from the Reformation on the Continent but was affected by the latter from the viewpoint of those who did not believe the Church of England had gone far enough to disassociate itself from "papism."
This leads us to the longer-term effects of the split within Western Christianity. If people were permitted to question the established form of Christianity, the implication, eventually, was that Christianity itself could be looked at, evaluated, and questioned. It is a controversial point but one that arguably is valid that the European Enlightenment, occurring two centuries after the Reformation, was in some ways an outgrowth of it. There were so many complex changes taking place in Europe from 1450 on that it's difficult to isolate one factor, even one as sweeping as the Reformation, as the cause of another other particular movement or phenomenon. One could counter that the invention of printing had just as great an effect, or was itself a cause of the Reformation. The religious division in Europe can also be seen as a stimulus for the colonization of the New World—or at least of North America, populated largely by religious dissenters who were escaping discrimination and persecution. This, too, was a long-term side effect of the chain of disputes that engulfed Europe in the aftermath of the Reformation.