I would invoke two things in relation to this. One is, that, according to many, God gave us all free will. That means we have the right and even the duty to make our own decisions for ourselves (and not have others make them for us). So, while the Church may preach that one should not use contraception, they can't FORCE you to do so.They rely on each individual's free will to make that decision (after arguing their case, of course). The same with anything that violates a religious tenent, including murder. You can't force people not to kill each other, but you can give people the information to make what you feel is an informed decision and hope they follow a responsible path. If I don't believe in murder because its against my religion, can I get out of paying the part of my taxes that goes to prisons?
The second is the protection of individual rights. The law is very clear that issues of contraception or abortion really are individual rights and decisions that can be made only by the direct parties. Religion informs how people make decisions, but cannot and should not (in our country at least) dictate directly. Given that a Catholic entity can and does employ non-Catholics, the DENIAL of these health coverage OPTIONS would be a serious infringement on their rights. And I do know at least three people who work for Catholic entities (Catholic Charities and a Catholic Secondary School, specifically) who are not Catholics, so this definitely happens and would be a serious infringement of their civil rights to deny them access to contraception.
Lastly, its worth noting on this contraception issue the recent study I cited in another forum that found "98 percent of sexually active Catholic women use or have used birth control other than church-approved natural family planning."
This indicates the Chuhrch is quite a bit out of step with realities of its US members and that refusing to offer contraception through health care would be seen as detrimental to more than just the non-Catholic employees of the church.