According to the Huffington Post:
A statement posted on a website claiming to be the official homepage of the Italian branch of Anonymous said the takedown was orchestrated in protest of a number of alleged abuses by the Catholic Church including past execution of heretics, the selling of indulgences, and the recent child abuse scandals involving priests.
"Today, Anonymous has decided to put your site under siege in response to your doctrine, liturgy and the absurd and anachronistic rules that your profit-making organisation spreads around the world," the hackers wrote in the statement, according to Reuters. "This attack is not against the Christian religion or the faithful around the world but against the corrupt Roman Apostolic Church."