Bryan Cones, managing editor of U.S. Catholic  magazine, muddies the emotional debate about the HHS ruling about contraceptive coverage with a few facts, namely the difference between a canonically Catholic organization and one with a Catholic connection that is more "historical and aspirational."
"All 'Catholic' institutions are not created equally, legally or even canonically speaking," he writes in a blog post titled, "Just which Catholic institutions are 'mandated' to provide contraception?" 
Among those exempted by the law, Cones says: Catholic parishes and schools, diocesan agencies directly connected to the bishop, religious congregations, most Catholic high schools and some Catholic colleges and universities (those for whom Catholic religious education and spirituality are required components).
Basically, it's hospitals, large universities and that serve and employ primarily non-Catholics, and possibly Catholic Charities because it is incorporated separately from the local church and not directly funded by it.
Cones doesn't say it, but I suspect the reason these larger organizations do not have such direct connections to the church is so they can receive government money. Unfortunately in this country you can't have it both ways.