The Habsburgs were synonymous with Catholic religion, it's widely known. They were fierce advocates of counter-reformation. They spread Catholicism violently in Bohemia after the battle of the White Mountain in 1620, and forced the Protestants to either convert or leave. They fought against largely Protestant rebels in Hungary and were mostly supported by the Catholic aristocrats there. They also suppressed Protestantism among their own nobility in Austria and promoted Catholics.
http://www.habsburger.net/en/chapter/fa ... lic-church
In the 19th century when Europe was turning secular, Catholic Church still had a lot of power in Austria and was serving to legitimize the Habsburg dynasty and their regime. The Orthodox Serbs fought against them and felt that Habsburgs were Catholic imperialists.
The Pope even beatified the last Habsburg ruler Charles I.