By taking the crown from the pope and crowning himself, Napoleon was showing that he held the superior power and the church's standing in France was through connection to him.
In 800, Charlemagne was crowned as the first Holy Roman Emperor by Pope Leo III. The ceremony marked an alliance between the papacy and Charlemagne as the king of the Franks. In subsequent years, other Holy Roman Emperors would also be crowned by popes. There was also an idea throughout Europe that rulers received their right to rule directly from God -- the idea of "divine right monarchy." So having an official of the church crown a king gave such divine indications to the ceremony.
In France during the Revolution, the church has been attacked as an enemy of the state. When Napoleon came to power after the French Revolution, he showed a willingness to restore the Catholic Church as the national church in France -- but in a way that made clear that the church was to serve the purposes of the French nation and, later, the French empire. The Concordat of 1801 was Napoleon's agreement with the Catholic Church. When he was taking the title of emperor in 1804, the pope, Pius VII, was there for the ceremony -- but the coronation was Napoleon's own action. He represented the center of power in France, and the church was subordinate to him.
