Going back to what we discussed earlier: Has Obama waged a War on Religion?
And this is where things get complicated.
Bear with me here, I think I'll arrive at a point at the end.
1. The constitution is for the most part structured to support "negative" rights, ie. the right to free speech, it means you cannot be censored by the government for saying what you believe. A notable exception to this is the right to bear arms, but it still fits as it does not obligate others to aid you in exercising these rights. The idea of "negative" rights is favoured by most classical liberals such as Objectivists (But please let's leave them out of this, they're only an example) and Libertartians.
2. Following the civil rights movement of the 60s and the passage of the various civil rights bills people now have "positive" rights, which are the right to do certain things. ie black people have the right to be treated the same as white people. This view is endorsed by the "progressive" movement which wants the government to guarantee equality, not protect rights.
3. This is where the problem emerges, people have the right not to be forced to work for all people if they don't wish to. ie a store can refuse to sell to black people. They can do this because it does not violate any "negative" rights because traditionally one did not have the right to eat at a certain restaurant. However civil rights legislation says you do, which leads to fun in the supreme court as the libertarians and progressives argue over which side has primacy on this issue.
4. And that is what we see in the above article. The church has freedom to follow its religious requirements, but according to the law the people also have the right to get contraception from their counselors.
So can a church be compelled to violate its' religious beliefs to make certain that the people have access to contraception?
If Obama says yes then he is violating their right to freedom of religion, unless there is a ruling somewhere like the one we have here in Canada that you have the right to freedom of religious belief but not to religious action. However if he does not guarantee said people access to contraception then he comes under fire from the progressives who elected him. In short he chose to further alienate those who dislike him, instead of those who are voting for him.
There is also mention of pulling government funding for these programs. Is this a problem? Not in my opinion. The government is looking to make sure all the services they want are provided, and if a church cannot provide them then the government should find someone else to do it. However if they are dropped because of their religion then it is an issue.