From a story located at:
The ruling is correct, if the institution resisting the ACA mandate, didn't take a single penny in common tax dollars. Religious schools, taking no tax dollars for operations are free to teach religion in their classrooms. Upon acceptance of common tax dollars, they lose their freedom to subject children of multi-cultural and religious backgrounds to a particular belief.
The Catholic Conference accepts millions of dollars in common tax dollars every year. They do wonderful work but the level of their services would be far less without tax dollars funding many of their operations. In addition, the Catholic Conference employs many people of different faiths because skilled employees come before "Catholic only" employees for efficient operations.
The Catholic Conference is not just a private religious organization. The Catholic Conference relies heavily on all citizens in our country to fund their good work. As such, because of their acceptance of public money and their willingness to employ people of all faiths, the Separation of Church and State applies. If the Catholic Church doesn't like the Separation of Church and State concept, envisioned by our Founding Fathers, then stop taking common tax dollars to help line the pockets of church authorities.
Accepting taxpayer money does not allow the Catholic Church to disregard Federal law to the detriment of its non-Catholic employees. The ACA is the Law of the land and all citizens are afforded equal protection under the law.