UPDATE (7 Feb at 7:00p): This is a nice roundup of both the reasons and related resources: Six Things Everyone Should Know About the Obama Mandate
UPDATE (22 Jan at 8:02p): This is a scathing article by liberal Catholic (i.e., he doesn't agree with the Catholic position here), Michael Sean Winters. He sees the problem with the HHS mandate, too, and it's not because he's defending the Catholic position on contraception (neither am I here), but because he sees it for what it is--an attack on religious liberty.
This morning before I got up and got to shoveling snow, I came across this bulletin from the USCCB about their intent to continue fighting the contraception mandate by the HHS. I tweeted it, saying I don't get why Barack Obama hates freedom of religion, noting how he is the most anti-First Amendment president in history. I say this because this is only one case where his administration has been fighting against it. Some others, for example: here, here, here, here, and here. These are just the ones I know about, and it's not like I watch this stuff full time.
I have had a few friends first question how this impinges on religious freedom and second why it matters (or rather, they feel it's not important).
1) First, whether or not you agree with us on the morality of contraception (we can set that discussion aside for now), let's at least acknowledge that the settled--by Pope Paul VI's 1968 encyclical Humanae Vitae, confirmed in the Church's universal catechism (2366-72), by Pope John Paul II in his great encyclical Evangelium Vitae, and reiterated innumerable times by our own bishops--Catholic position on the matter is that the use of artificial contraception is immoral. In other words, our religion clearly and unequivocally teaches that artificial contraception is immoral. (And add to this that some of the regulated contraception is known to be abortifacient, so this is also about abortion, another thing clearly immoral in Catholic doctrine.)
2) Now let us also agree that the new regulation says that Catholic organizations must provide artificial contraception in their health plans.
3) Given 1 and 2, what this boils down to is the government forcing a religious organization to fund something that is directly opposed to its own belief system. This is patently unconstitutional, a clear violation of the free exercise of religion. Free exercise includes not being forced to do things that your religion says are immoral. This article also deals with some of the finer points involved.
The violation of free exercise is pretty clear to me. The only thing I can figure is that those who don't see the mandate as a problem can't believe that we really think artificial contraception is a moral evil. I understand why this is hard to believe in our culture, but hopefully if you glance at some of the links above, you'll see that, yes, we really do think contraception is immoral, notwithstanding the fact that many Catholics choose to ignore this clear doctrine.
For my wife and I, as converts, this was a difficult one to come around to, and it was in part a reason we shied away initially from becoming Catholic, even though we were pretty convinced we should. You see, we think that if we profess to believe something, we should act accordingly, even when it is difficult, and so we knew that if we were going to become Catholic that not using artificial birth control is part of it. (Of course, that puts it negatively--the reasons artificial contraception is not to be used are derived from a much more positive, holistic, and healthy view of sexuality than what our contemporary culture offers.) It was in fact Evangelium Vitae that helped me to come around--because it situates this question in the broader Catholic understanding of the dignity of life.
But I digress, the point is that whether or not you agree with the Catholic religion's position on artificial contraception, it is a real moral, religious doctrine, just as much as that which says "thou shalt not kill." And forcing Catholics--including Catholic organizations who help non-Catholics--to participate in something we believe to be immoral precludes our free exercise of our religion. It's as simple as that.
A while back, I was pointing out other infringements on religious liberty, ones that are forcing overwhelmingly good social services out of business (e.g., here and here--same has been happening in the UK). The defense of this kind of stuff says, basically, it's not a violation of free exercise--we can always just, essentially, not help people. What kind of a choice is that? Not to mention, our religion also explicitly teaches us to care for the poor, the orphan, and others--so we are in effect being prevented from doing that in these cases. How many unfortunates are we putting at risk due to these ideologically motivated attacks on religious freedom? A lot--Catholic charitable organizations serve more people than any other in the world.
This is also important because it goes to the core of who we are as a country. You may not see this particular issue as important to yourself, but it is one among other increasing impingements on this first American liberty. All that is required for the triumph of evil is for good people to do nothing. All Americans should be concerned about this. Today it's artificial contraception. What will it be tomorrow? How many times must our freedoms be denied before you take action? Will it be too late then?