In 1796, Napoleon invaded Italy and defeated the papal army. The French troops took Pope VI prisoner and he died in captivity seven months later.
The risks to a politician in antagonizing such a powerful entity as the Vatican are enormous while the tangible benefits are little. Unlike other colonized countries, the Vatican does not have much natural resources or workers to exploit. However, being a major religion in Europe, the support it holds in the European population is mighty. Even today when the political power of Christian leaders has waned compared to hundreds of years ago, very few(or zero) Western leaders dare to offend the Church. It does not look like a smart move by Napoleon to antagonize the all-powerful Catholic Church unless there are huge advantages to be gained.
What advantages did Napoleon gain by attacking and antagonizing the Catholic Church?
This question assumes that Napoleon was a shrewd politician who made calculated moves and not a hot-tempered person who makes decisions on his whims (I don't like you, so I attack).