Short answer: Napoleon realized that the French Revolution's attack on the Catholic Church went against the desires of the majority of France's people. So he restored the Catholic Church as the official religion of France ... but with assurance that it would be loyal to his government.
Context/detail:
In France during the Revolution, the church came to be seen as an enemy of the state. Church lands were seized, and many clergy members were imprisoned and even executed. The masses of the French people were Catholics, and so some of these moves were deeply unpopular with the common people.
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.
