Imagine a large institution that provides free meals to the poor, and imagine that the institution is run by Jains, who are vegetarians. None of the meals offered by this institution include meat, though many of the people to whom the meals are offered are neither Jains nor non-Jainist vegetarians. Now imagine that the federal government (never mind under which agency) issues a rule that requires any organization that offers the poor free meals to include meat on its menu, with the single exception of religious organizations that offer only coreligionists free meals. In the statement announcing the new requirement, the government points out that most people do eat meat, and that most doctors believe meat is good for you in the right amounts, since it provides important nutrients that are difficult to find in other foods. The statement does not mention that most people find the Jains' arguments against eating meat bizarre and irrelevant (it doesn't need to). Like other vegetarians, Jains are eager to point out that it 's possible, though more difficult, to get the proteins meat provides from other foods, and that eating meat involves other health risks. Defenders of the new rule insist the government is being asked to indulge a sectarian scruple at the expense of public health.
Now, does one have to believe it's wrong to eat meat -- for the reasons adduced by Jains or for any other reason -- to believe that the government should not force Jainist soup kitchens to offer it? I don't think so. I don't agree with Jains about vegetarianism (though I do think there are formidable moral arguments against eating meat), just I am not persuaded by the reasons offered by my own church for its teaching about contraception (though I think there are formidable non-moral arguments against the pill). But I also don't believe it's the federal government's job to decide whether Jainism's arguments for vegetarianism or the Catholic Church's arguments against artificial contraception are worthy of respect or accommodation. Nor does it matter how small a part of the general population is vegetarian, or even how many Jains quietly ignore their religious community's doctrine. (Let us stipulate, for the sake of this imperfect analogy, that Jainism teaches not only that Jains shouldn't eat meat, but also that it is wrong for them to be complicit in the meat-eating of other people; perhaps it doesn't.)
If the only permissible expressions of religious freedom are those that do not conflict with the surrounding secular culture, then religious freedom is an empty phrase. If religious freedom means only that everyone is free to have different religious reasons for doing what the state expects everyone to do anyway, whatever they believe -- or if it means only that one may worship a god of one's choosing however one likes so long as one serves one's chosen deity in a way that neatly corresponds to the priorities of the state -- then the principle of religious freedom is no more than decorative.
By not serving meat, the Jainist soup kitchen isn't forcing anyone to become vegetarian, or withholding something to which the people they serve have a right. The right to eat meat does not entail the right to be served meat by Jains. The Jains' willingness to serve hungry people food that will keep them alive and healthy does not oblige them to serve them every food approved by nutritionists, even if the nutritionists are confident that the people the Jains serve would be healthier at less expense if the Jains expanded their menu. If the government thinks the free provision of meat is an urgent public good, the government must arrange for that provision itself, and not simply mandate that other institutions provide it (or provide nothing). Long ago Americans decided that education was something that all children in this country were entitled to, whether their parents could afford to pay for it or not, and so we created a public-school system. Call it the default public option for education. The government also regulates private schools, but it does not insist that they have exactly the same curriculum as public schools; it doesn't need to, precisely because public schools are available to everyone.
If we are going to speak of health care as something to which all are entitled, no matter how much money they have (and I believe we should speak of it this way), then we need to make sure a default public option for health care is available to everyone. This option could cover whatever the government believes health insurance ought to cover -- including, perhaps, some things that certain religions disapprove of. People could still get private insurance that covered a little less or a lot more, just as people can still send their children to private schools. But the government would no longer be in the awkward position of demanding that other institutions offer some public good only on the government's terms while failing to provide this good itself.