Legal challenges to the contraceptive mandate in the Affordable Care Act (ACA) raise important questions about religious freedom -- but not the ones the plaintiffs emphasize.

There are two separate issues. The first is how broadly we define "houses of worship" when we decide which religious nonprofits get an exemption from the mandate. The second is whether we think for-profit corporations have religious rights like individuals do. And if so, whether those rights outweigh the right of employees to make moral decisions about their own health care.

The First Amendment protects religious freedom in two ways. It prevents Congress from passing any law "respecting an establishment of religion, or prohibiting the free exercise thereof." It's "free exercise" that's at stake here.

The plaintiffs say that requiring insurance plans to cover contraceptives violates the free exercise rights of employers who morally object to some or all contraceptives.

They argue, citing the Religious Freedom Restoration Act of 1993 (RFRA), that the mandate unconstitutionally infringes their right not to fund or promote medical procedures they consider immoral. RFRA recognizes that government may enact policies that have the unintended effect of infringing religious freedom -- child welfare laws, for example, prevent some religious schools from beating children with a rod though some verses in Proverbs advise it. In such cases, according to RFRA, the government must demonstrate a compelling government interest and show that it's met in the least restrictive way -- easy in the case of child welfare, much less clear in the case of contraceptive coverage.

The Department of Health and Human Services (HHS) requires health insurance plans to cover contraceptives at no cost because the Institute of Medicine (IOM), an independent nonprofit organization that gives medical advice to the government, recommended that contraceptive care be included in the list of basic preventive services covered at no cost by insurance policies under ACA.

The compelling government interest is straightforward.

Women have a constitutional right to decide whether and when to bear children. They have the right to make decisions about their own reproductive health, including whether to use contraceptives. The Supreme Court decided that almost 50 years ago in its landmark ruling, Griswold v Connecticut. By providing free coverage, ACA expands the ability of women, whatever their economic circumstances, to exercise this fundamental constitutional right. But there are other issues.

In our society women usually bear the bulk of responsibility for birth control, though women, men, and their children all benefit from family planning. That means the economic burden of this general social good falls disproportionately on women. ACA seeks to correct this inequity by spreading the cost of contraceptives -- and pregnancy care and childbirth -- across the entire insurance pool, putting an end to the higher price women pay for basic health care, either out-of-pocket or through higher premiums. It's an issue of fairness, but it also promotes the physical and economic health and well-being of women and their families.

Some of the medications and procedures that are effective for birth control also have other positive health benefits for women and the children they bear.

Finally, by lowering the number of unplanned pregnancies, contraceptives reduce the number of abortions, a result that is good for the health of women and for the overall cost of health care, aside from the moral issues involved.

For all these reasons, HHS followed the advice of IOM and required insurance plans to provide free contraceptive coverage.

They met a clear and compelling government interest. But did they do it in the least restrictive way?

If you think "free exercise" rights are for individuals, the answer clearly is yes. Each person is free to choose according to his or her own conscience whether to use this form of medical care. Roman Catholics of child-bearing age who follow the teaching of the Magisterium have the religious freedom to refuse this care, and others -- like my family -- who have no moral objection can take advantage of this basic preventive care when appropriate, whatever their economic circumstances.

This is the beauty of the First Amendment. Moral choices and religious convictions are left to the individual.

But the issue is complicated by an American health insurance system that relies heavily on employer-provided private insurance.

What do you do when an employer's moral convictions differ from those of her employees? Whose conscience carries greater weight under the First Amendment?

There's considerable legal precedent exempting churches and other "houses of worship" from laws that are generally beneficial but may violate core religious teachings. You can sue your boss for refusing to promote you because of your gender, but you can't sue your church for not ordaining women if that's their teaching.

HHS realized the contraceptive mandate would pose a moral problem for some churches, so it created an exemption for "houses of worship." Initially, HHS said that religious nonprofits like hospitals, universities, and charities weren't exempt. Catholic bishops and church-related universities and hospitals objected. A group of religious leaders worked behind the scenes with the White House to craft a compromise. Under the new rule, religious nonprofits who object to contraceptives don't have to pay for or arrange contraceptive coverage for their employees. They simply inform their insurer of their religious objection and the insurer, not the employer, notifies employees (or students) that it will offer contraceptive coverage in a separate policy at no cost. The religious freedoms of employer and employee are protected.

I thought the compromise was Solomonic. The U.S. conference of Roman Catholic bishops disagreed.

Perhaps they agree with the Little Sisters of the Poor in Colorado that the very act of claiming the exemption violates their religious freedom. I'm not sure. But I don't get it.

The Hobby Lobby case raises a much more fundamental issue, with a much more troubling possible outcome.

Hobby Lobby is a for-profit business, not a "house of worship" or a religiously-affiliated nonprofit. Business owners can believe whatever they want to believe, but in their business activities they must obey the law even if they disagree with it. A restauranteur, for example, has the right to believe that same-sex marriage is wrong and to preach that gay and lesbian people need to be rescued from their sin; but in his restaurant, he can't refuse to serve people he thinks are lesbian or gay. The owners of Hobby Lobby have a right to believe that certain contraceptives are morally wrong. But as a for-profit business, Hobby Lobby does not have the right to make that moral determination for their employees.

The HHS rule was made for sound medical reasons to serve a compelling government interest. It leaves moral decisions about using contraceptives to individual citizens, exactly as it should. The owners of Hobby Lobby should not make those basic moral and religious decisions for their employees. They have religious rights as individuals, but their rights as employers do not trump the religious rights of their employees. In America, we don't give up our right to make our own moral choices when we take a job. This is a basic American principle that goes to the heart of our national identity.

From the time the first Christian state church was established in Armenia in 301 to the Peace of Westphalia in 1648 that ended the religious wars of Europe following the Protestant Reformation, the conventional view was that the religious convictions of kings, emperors, and princes rightly determined the religious beliefs and practices of their subjects.

Early Americans disagreed. They followed the example of Baptist theologian Roger Williams who founded the colony of Rhode Island on a principle of unlimited religious freedom. Inspired by the writings of the English philosopher John Locke and their own Thomas Jefferson, early Americans followed Williams' example and lodged the right to moral conscience and religious freedom squarely in the individual citizen. This American view was incorporated into the Universal Declaration of Human Rights.

If the court rules for Hobby Lobby, it will undermine religious freedom as Americans have understood it from the beginning of our nation. It will shift free exercise protections from the individual to the heads of the corporations that employ us. It will set a very dangerous precedent that will have bad consequences for the free exercise of religion, granting power to our employers that once was held by princes, kings, and emperors and infringing our First Amendment right to make our own moral decisions.

Where will it stop? If Hobby Lobby can ban contraceptives the bosses find morally objectionable, will other employers have the right to exclude blood transfusions or hospital care because their faith traditions say such things are wrong?

We fought a revolution in part to give individuals the right to make their own moral and religious decisions. I pray we don't go backwards on religious freedom.