Pope Julius II is called the "Warrior Pope" because he is the only pope ever to lead troops into battle. The fact that he did this shows how much the Church was involved in Italian politics.
During this time, the Pope was not simply the head of a church, but also the temporal ruler of the Papal States. The Papal States were one of the many little states that made up what we now call Italy. All of these states were jockeying with each other for increased power. In the course of these competitions, they would also bring in foreign powers like France. Therefore, there was a great deal of conflict going on between various states at essentially all times.
The Church itself (as a spiritual entity) was also deeply involved in these conflicts. The Pope would, for example, use his power as the head of the Church to try to advance his temporal goals. He used his power of excommunication against King Louis of France at one point in an attempt to weaken France and its allies. At the same time, these allies were trying to overthrow him and set up a new pope.
In these ways, it is clear that religious and secular concerns were very much tied up with one another. This helped to create the turmoil that wracked Italy during this time.