Sarah Posner at Salon does a pretty good job of describing why this is almost always the case with this president:

After decisively issuing the contraception coverage rule last week, the administration took only a few news cycles, dominated by liberal Catholics like E.J. Dionne fretting about how Obama "botched" the issue, to dispatch surrogates to assuage the U.S. Conference of Catholic Bishops.

"There are conversations right now to arrange a meeting to talk with folks about how this policy can be nuanced," pastor Joel Hunter, a conservative evangelical who is close to the president, told the Washington Post on Tuesday. "This is so fixable, and we just want to get into the conversation." The bishops promptly signaled that they would reject the floated compromise out of hand.

[snip]

The Obama administration -- not unlike its predecessors of both parties -- looks out with blinders at the religion landscape. The blinders extend no further than the religious groups with lobbyists (like the bishops) in Washington, who claim to represent their entire religion, even when, for example, 98 percent of Catholic women don't seem to care that the bishops insist contraception is a sin. As a recent study by the Pew Forum on Religion and Public Life showed, the money to lobby can buy you access to ensure your religious views -- even if they contradict medicine, science or public health -- shape policy. As Catholics for Choice has pointed out, though, Archbishop Timothy Dolan doesn't represent all American Catholics, but rather the 271 American bishops.

I am, quite frankly, achingly tired of male religious leaders, male politicians and male leaders of religious/conservative interest groups sucking all the oxygen out of the room whenever it is women's reproductive health and decision-making on the table, and refusing to hear the loud and definite voices of the millions of women - including Catholic women - who feel they have a right to have a say in their health care.  There is no "compromise" in the Catholic Bishops, which inevitably means that Obama is going to "reach out" and serve religious freedom by allowing the imposition, in some way, of religious doctrine on many women who don't share that doctrine - and we know what that means in the end: women suffer.

If you're a Catholic school or hospital, and you employ non-Catholics, and you serve non-Catholics in the community, and especailly if you take one dime of federal money, your employees need to have the same right to coverage for contraception as they would with any other employer.  Being handed a pamphlet or given a number to call, to find out how to obtain a rider, or obtain coverage is humiliating to the employee, and, in my opinion, a violation of privacy.  If men had to go get a pamphlet or get a phone number for where they could get coverage for or obtain drugs for ED, well, what am I thinking: THAT WOULD NEVER HAPPEN.

As Posner says,

Obama would do better to govern and to run for reelection as a frankly secular candidate: the president who will ensure that policy is made based on reason and science, not religion. And he should make clear that he comes to this position precisely because he cherishes the free exercise of religion (or not) of all Americans. While this might cause indignation among some of those with a seat at the Washington table and set off fainting spells on cable news, it would not cause Obama to lose critical swing constituencies such as white Catholics or moderate evangelicals.

Given how handy we women are as political footballs, I don't imagine we're going to get to know Obama-the-Secular-Candidate/President anytime soon.