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The era of the Crusades certainly coincides with a dramatic increase in the authority of the Pope, both in practical terms and in the development of doctrine. It is a bit hard to untangle how much of this is due to the Crusades themselves.
First, a word of warning! It is very easy to slip into anachronistic habits when thinking about the medieval papacy. It is often confused with:
Another word of warning: it's tempting to imagine that this history is the result of a single papal master plan to increase their power, a sort of conspiracy theory. Actually, individual popes differed enormously in their personal beliefs about the role of the Church and the Papacy, let alone their ability to implement them.
In the following, I'll explore the relationships between the See of Rome and other contemporary powers: the Emperor, other rulers, other bishops (as well as abbots and so on) in the Western church, and the patriarchs of the Eastern sees.
The overwhelmingly most important power conflict was with the Emperor. This was the struggle that animated contemporary political theory, as well as the grounding theology of the Pope's temporal power. Both parties claimed a kind of supreme authority (as well as claiming to be the legitimate heirs of the Roman Empire) and so it was quite the puzzle to decide who was allowed to tell the other one what to do, and who appointed new Popes or Emperors. The doctrine of the "two swords" divided their responsibilities - but not like our modern idea of the separation of the church and the state. In the version of Bernard of Clairvaux (enlisted by Eugene III to preach support for the Second Crusade) there is a spiritual sword, belonging to the Pope, and a temporal sword, in the custody of the Emperor, but ultimately subject to papal authority. The church does not fight, but it commands.
A good example here is Innocent III's decree Per venerabilem (1202) which asserts a papal power to supervise the Imperial election, since he sees the institution of the Empire as a creation of the Church. Innocent III was not only a reforming and monarchical Pope, but also the one who called the Fourth Crusade, and excommunicated Otto IV. Although the Empire became a less relevant political force in later years, the contest between Empire and Papacy (partly driven by the issue of control over the Crusades) did help to solidify the doctrine of papal supremacy.
In the same way, other rulers were meant to have a duty to fight for the Church when requested (on pain of deprivation of Communion, at the least, according to Gratian). This applied to the suppression of heresy, and to the Crusades in the East. The duty was not the same as the normal feudal obedience, though; it applied even to those who did not have a cleric as their feudal lord (such as the papal possessions in central Italy that were to become the Papal States). But in practice, it's not like a bishop could just turn up at a castle and start telling the king what to do, especially when the king considers the bishop to be one of his subjects. Perhaps he even nominated the bishop to the see, and expected regular tax payments rather than being asked to pay some sort of crusading tax in the other direction.
So crusades tended to create local political crises of this kind: and in the long term, the Church was able to negotiate a standard where clergy were in a sort of parallel legal world. They had their own law (canon law), their own system of taxation (tithes and so on), and their own hierarchy of loyalty. Although much of this was systematized at the Fourth Lateran Council, under Innocent III once again, it had been a long time in the building.
It's easy to take for granted, now, the extent to which local diocesan bishops are subordinated to Rome. In the past, bishops (and abbots) were much more independent - legally, in the scope of their ability to make law for their diocese; and politically, in the power they could draw from tithes, assignment of benefices, and so on. During the time of the Crusades, the papal curia developed into an institution that was not just for the Pope's household and his diplomatic efforts, but was a bureaucratic organ for the whole church. Increased centralization was at the expense of bishops' autonomy. It's hard to say if this was "because of" the Crusades, but there are some key points that helped:
The obvious doctrinal roadblock to Papal supremacy is the fact that there were all these other Patriarchs in the East, who thought that the Pope was first among equals, rather than being a level above. Calling a Crusade at all is a direct assertion of a Pope's universal authority, since it invoked papal jurisdiction outside his traditional territory. During the era, there is a shift from the First Crusade (partially justified by the idea that Constantinople had asked for help from the West) to the Fourth (in which Constantinople was sacked); put crudely, people in the West cared less about what the Eastern Church wanted. The ultimate failure of the Crusades to maintain Christian hegemony over the Near East meant that the Patriarchs were in no position to challenge claims of papal authority in the Western Church.
The papacy was no longer a merely local institution, but a prize which was definitely worth fighting over. After the Crusades come the exile in Avignon, the Western Schism, and conciliarism - all of these represent attempts, by one party of another, to control the papacy. In the longer term, the increased centralization and organization of the Church ultimately created its own internal challenges to unfettered papal authority. Among these are:
Again, there were and are many schools of thought about exactly what the scope of papal power ought to be. The Crusading era saw the emergence of a particularly strong version of the doctrine of papal authority, which the Popes were ultimately unable to maintain, but which is in continuity with the present forms and structures of the Roman Catholic Church.
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I won't comment on the popes' intentions but sending European kings and nobles and large segments of their armies to fight a foreign war meant there were fewer people left in Europe to challenge their authority. People supported the early crusades because they were trying to save Eastern Christians and holy places from the Turks. Thus people were more supportive of the popes for leading them in a holy war.
The increased support during the 11th and 12th centuries was certainly a factor in the increase in secular political involvement and financial excesses noted in the 13th and 14th centuries. The combination of secular politics, criticism, and the schism surrounding the Avignon papacy laid the foundation for the protestant reformation.