As Europe came out of the Middle Ages, stronger governments were able to better control their people and geographic areas. Why?
This question relates to a theme which runs from the Early Modern Era backwards across the Middle Ages: feudal lords and rulers ultimately had competing interests, with Rulers seeking to centralize power under themselves, while the Lords sought to protect their own traditional rights and privileges. Also note that this conflict could turn violent, and struggles between lords and kings did have the potential to spark a civil war.
There were trends within the High Middle Ages which might be worth discussing as far as this question is concerned. The High Middle Ages saw dramatic population growth, bringing with it revivals in trade as well as the growth of towns. I would suggest these evolutions were ultimately to the advantage of the monarchs, given that increased centralization appears to have been a theme of the Late Middle Ages. To quote one historian:
Feudalism finally waned in the monarchical states in the late fourteenth century with the emergence of stronger state structures, as well as the reimposition of the authority of the Roman Catholic Church in much of Europe. Thus, feudal relationships dissolved as the strength of rulers increased and the independence of nobles declined. [John Merriman, A History of Modern Europe: From the Renaissance to the Present (Third Edition). New York: W. W. Norton, 2010, p. 12]
In addition, consider the impact of the Black Death, which further devastated feudal structures across Europe.
In any case, it was with the Early Modern Era that we observe the rise of bureaucratic absolutist states. Here, we see centralization closely tied with warfare. Gunpowder technology was critical to this, in that it destroyed the traditional role of the nobility in warfare. These technological advancements culminated in the rise of Standing Armies, which enforced but also necessitated the growing power of the state. Standing Armies on a national scale require a high degree of bureaucratization in order to function. Political centralization and military necessity tended to go hand in hand.
The major reason for this was the decline of the feudal system. As feudal lords lost power, monarchs were able to take greater control of their territories and people.
The decline of feudalism came about for at least two main reasons. First, there was the increase in trade and in the economic importance of the middle class. This made cities more important and agricultural manors less important in economic terms. Second, there were changes in military technology. The rise of such things as longbows and even gunpowder made knights much less militarily valuable. Large armies were now much more important than individual knights. These two trends combined to make feudal lords much less important both militarily and economically. This allowed monarchs to keep greater control of their territory.