What's worse for the president, the suits have been filed in an election year, and have a decidedly political edge. New York's Cardinal Timothy M. Dolan, who gave the invocation at the Republican National Convention in Tampa, Fla., is a leading plaintiff.
Dolan's office said last week his RNC appearance was not an endorsement, and he gave the invocation at the Democratic National Convention as well.
Nevertheless, Catholic bishops simply do not want employees of religious institutions to be guaranteed contraception coverage in their employer-provided health insurance. Official Catholic doctrine bans artificial birth control -- as opposed to Natural Family Planning, which relies on sex during infertile periods, as opposed to the old "rhythm method," which relies on estimating menstrual cycles to prevent pregnancy.
Only in the mid-20th century has Catholic doctrine conceded even married couples could have sex for purposes other than producing children.
One of the mandates in Obama's Affordable Care Act, part of its preventive care provisions, requires religious hospitals, schools and charities to include co-pay-free birth control in their employer-provided health insurance coverage. Churches, such as Catholic parishes, are exempt.
The mandate has caused in uproar in the Catholic hierarchy, which rejected an administration compromise requiring insurance companies to pay for the contraception coverage, not the religious institutions.
In May, 12 lawsuits challenging the mandate were filed involving more than 40 Catholic organizations.
The Catholic organizations include Dolan's Archdiocese of New York, the University of Notre Dame and Catholic Charities of the Archdiocese of Chicago, the conservative American Center for Law and Justice said.
The ACLJ, founded by the Rev. Pat Robertson, has filed briefs in all 12 cases opposing government motions for dismissal. The organization also filed friend-of-the-court briefs in all the cases on behalf of 79 members of Congress.
In a statement, senior ACLJ counsel Edward White said, "The mandate devastates the religious freedom of all employers seeking to comply with their religious beliefs. This is not just an issue negatively impacting Catholics. This is an issue negatively impacting employers of all faiths."
The president of Notre Dame, the Rev. John Jenkins, explained his university's suit this way, Commonweal reported.
"Today the University of Notre Dame filed a lawsuit in U.S. District Court for the Northern District of Indiana regarding a recent mandate from the U.S. Department of Health and Human Services," Jenkins said in a letter to the university community. "That mandate requires Notre Dame and similar religious organizations to provide in their insurance plans abortion-inducing drugs, contraceptives and sterilization procedures, which are contrary to Catholic teaching. The decision to file this lawsuit came after much deliberation, discussion and efforts to find a solution acceptable to the various parties."
He continued: "For if one presidential administration can override our religious purpose and use religious organizations to advance policies that undercut our values, then surely another administration will do the same for another very different set of policies, each time invoking some concept of popular will or the public good, with the result these religious organizations become mere tools for the exercise of government power, morally subservient to the state, and not free from its infringements. If that happens, it will be the end of genuinely religious organizations in all but name."
Not all Catholics appear to agree with the hierarchy on the "moral acceptability" of contraception. A Gallup poll conducted May 3-6 of 1,024 adults indicated 85 percent of U.S. Catholics found contraception "morally acceptable" while only 15 percent found it "morally wrong."
The poll had a margin of error of 4 percentage points.
On the political side, Catholics appear to be much more divided. Gallup, in a poll of 1,915 Catholic registered voters in April -- with a 3 percentage point margin of error -- found Catholics evenly split between Obama and Republican rival Mitt Romney, 46-46 percent with 8 percent undecided. The poll was taken before the hierarchy filed suit.
After the U.S. Supreme Court upheld most of Obamacare last June, self-described "Catholic progressive" and abortion opponent Steve Schneck celebrated the decision in The Washington Post. Schneck is director of Institute for Policy Research and Catholic Studies at the Catholic University of America and a board member of Catholics in Alliance for the Common Good.
"This week's Supreme Court decision makes all of this more glorious," Schneck said. "Healthcare for almost all Americans! No more denial of coverage for people with cancer or other expensive conditions! Better healthcare for seniors! Medicaid coverage for the working poor! Extended family coverage for college-agers! A host of special programs [thanks to Democratic Sen. Bob Casey of Pennsylvania] for at-risk pregnant moms and newborns! The law is not perfect, of course. Some Americans such as undocumented immigrants aren't covered. But for Catholics, the ACA brings us close to what our church has pushed for since 1919. Hooray, hooray!"
He added: "Like many of those Catholics and other pro-lifers, I'm also gratified that decisions by lower courts have time and again affirmed the effectiveness of President Obama's executive order against any federal funding of abortions in the ACA. I'm grateful for the stalwart leadership of Democrats like outgoing Sen. Ben Nelson, D-Neb., and former Rep. Bart Stupak, D-Mich., in helping to insure that protection. The attorneys of the U.S. Conference of Catholic Bishops remain mistaken in interpreting the ACA's state exchanges as allowing federal funding of abortion."
Schneck's was a voice of reason before the lawsuits were fired.
"Surely there are ways within the law to provide contraception coverage to all who want it that don't require religious organizations to compromise tenets of their faith," he wrote. "Indeed, there are ways to exempt religious organizations completely while also providing more comprehensive contraception coverage than under the complicated tangle of existing ACA rules and accommodations. Religious organizations and contraception advocates can both cheer."
Meanwhile, Catholic bishops and institutions aren't the only ones filing suit against the contraception mandate.
Lyle Denniston, the veteran Supreme Court reporter writing in SCOTUSBLOG.com, said a religious college in Illinois asked a U.S. judge in Washington last month to protect it "from having to provide insurance for birth control and abortion for its employees."
That suit was dismissed, the judge saying the suit was premature because Wheaton College was granted a one-year exemption from the mandate.
Elsewhere, The Hill newspaper reported, Grace College and Seminary in Indiana and Biola University in California also filed suit, arguing "covering certain forms of birth control for employees without a co-pay amounts to 'participating in' abortion."
"The mandate imposes a substantial burden on the schools' religious exercise and coerces them to change or violate their religious beliefs," a complaint filed in federal court by the schools said.
All roads lead to Rome, and all big legal and political disputes lead to the U.S. Supreme Court -- which can turn them away or grant review.
So what have the justices had to say recently about religious institutions and their employees? In a case decided last January, quite a bit.
In Hosanna-Tabor Evangelical Lutheran Church and School vs. EEOC, the Redford, Mich., school is a member congregation of the Lutheran Church-Missouri Synod.
The synod classifies its school teachers into two categories, "called" and "lay."
"Called" teachers have been called to their vocation by God. To be eligible to be considered "called," a teacher "must complete certain academic requirements, including a course of theological study. Once called, a teacher receives the formal title 'minister of religion, commissioned,'" the Supreme Court said.
In contrast, "lay" teachers "are not required to be trained by the synod or even to be Lutheran. Although lay and called teachers at Hosanna-Tabor generally performed the same duties, lay teachers were hired only when called teachers were unavailable."
The case was brought by Cheryl Perich, a former teacher at the Lutheran school. She was a "called" teacher, but spent most of her time teaching secular subjects. Perich had taken a leave of absence to be treated for narcolepsy. She threatened to sue under the Americans with Disabilities Act when she was not offered her job back.
The school said she had violated a teaching that disputes must be handled by church authorities.
The Supreme Court ruled unanimously the First Amendment, with its provision guaranteeing the free exercise of religion, bars "suits brought on behalf of ministers against their churches, claiming termination in violation of employment discrimination laws."
Any suggestion "Hosanna-Tabor's asserted religious reason for firing Perich" was just a pretext "misses the point of the ministerial exception" outlined in the unanimous opinion. "The purpose of the exception is not to safeguard a church's decision to fire a minister only when it is made for a religious reason. The exception instead ensures that the authority to select and control who will minister to the faithful is the church's alone."
The suits filed by the Catholic bishops and Catholic and evangelical institutions aren't remotely analogous to Perich's case. But the opinion written by Chief Justice John Roberts shows how much deference the entire court is willing to cede to religious institutions as employers.
"The interest of society in the enforcement of employment discrimination statutes is undoubtedly important," Roberts wrote. "But so too is the interest of religious groups in choosing who will preach their beliefs, teach their faith, and carry out their mission. When a minister who has been fired sues her church alleging that her termination was discriminatory, the First Amendment has struck the balance for us. The church must be free to choose those who will guide it on its way."