Zack Beauchamp, writing on Andrew Sullivan's blog, has a well-argued explanation of how the Obama administration is not threatening the religious freedom of the Catholic Church by enforcing regulations on health insurance coverage:
Allowing "conscience" exemptions whenever an employer doesn't feel morally clean when complying with regulations in principle neuters all regulation. The argument for allowing Catholic hospitals a pass on covering birth control has to rest or fall on the specifics of the case rather than a general commitment to protecting "voluntary communities."
This is where the case against the Administration's ruling is at its weakest. Birth control is for 98% of women the principal means of protecting a right central to their own liberty - the right to choose when to create a family. Chances are most women employed by Catholic universities and hospitals are part of the 98%. For these women, not having access to birth control renders a crucially important right meaningless.
I'm fine with religious freedom. I am not fine with religious organizations taking public money, and then claiming special conditions on how they'll accept it.