In his book Notes on the State of Virginia, Thomas Jefferson famously observed, “It does me no injury for my neighbor to say there are twenty gods, or no god. It neither picks my pocket nor breaks my leg.”

Jefferson referred not just to his personal views, but to the nascent state of Virginia’s approach to religious liberty, which would be codified just a few short years later in the Virginia Statute for Religious Freedom.

That statute freed Virginians from being forced to support religious groups against their will and guaranteed all the right to affiliate with the group of their choice. Under it, “all men shall be free to profess, and by argument to maintain, their opinion in matters of religion, and that the same shall in no wise diminish enlarge, or affect their civil capacities.”

If the sentiment sounds familiar, that’s because this statute became the model for the First Amendment of the U.S. Constitution and shaped our nation’s legal approach to religious liberty. The Founding Fathers never intended for religious affiliation to impede an individual’s rights.

Fast forward to the 21st Century and the data is in: The United States has achieved an unprecedented level of religious diversity. But despite this trend and a historical guarantee of free religious expression, many Americans still experience discrimination on the basis of their religious affiliation – or lack thereof.

But despite all of the carping you hear from Religious Right activists these days about “persecution,” it isn’t conservative Christians who are bearing the brunt of this. Their rights are secure. For religious minorities and non-believers, it can be a different story.

Several states across the country still boast archaic laws banning atheists from holding public office. These laws, which were the subject of a recent New York Times article, aren’t enforceable but remain on the books, a stark reminder of days of bigotry gone by.

Sometimes, discrimination takes a more violent turn: The Federal Bureau of Investigation (FBI) reports that 17.4 percent of all hate crimes committed in 2013 occurred due to religious bias.

Visible religious minorities are particularly vulnerable. The FBI’s data shows that Jews and Muslims, who often wear religious garb, consistently rank as the two most frequently targeted religious groups.

The FBI, of course, focuses on crim­inal activity alone. But there are subtler forms of religious persecution in America. Employment discrimination, violations of the Religious Land Use and Institutionalized Persons Act (RLUIPA) and other First Amendment violations also contribute to the marginalization of a particular belief group – and both, critics say, threaten Jefferson’s vision of religious liberty.

Prisoners – the “institutionalized persons” RLUIPA is designed to protect – often bear the brunt of religious persecution, but it’s rare for Christian inmates to have problems behind bars. Indeed, some prisons and jails even sponsor programs designed to convert inmates to fundamentalism in the hopes they’ll go straight.

Inmates who belong to non-Christian faiths or who have atheistic beliefs often have a tougher time. According to established legal prece­dent, prisoners are entitled to certain religious accommodations while incarcerated. That includes the ability to access religious literature, participate in religious services, join in small groups and adhere to a religious diet.

These accommodations are still subject to restrictions based on the prison’s security requirements and the practicalities of providing special services (like kosher or halal food) to inmates. But First Amendment advocates say that prisons can take an unconstitutionally hard line on inmate religious expression, especially when the inmate belongs to a minority belief tradition.

The U.S. Supreme Court is currently examining this issue in a case from Arkansas concerning a Muslim inmate who is seeking the right to grow a short beard for religious reasons. (See “The Prisoner’s Dilemma,” May 2014 Church & State.)

Gregory Holt, whose interpretation of Salafist Islam requires him to wear facial hair, told the high court in a rare handwritten petition that he’d been repeatedly denied an accommodation for his beliefs.

Arkansas prisons currently permit only quarter-inch beards for inmates with skin conditions. Prison officials have consistently argued that allowing Holt to grow another quarter inch of facial hair would create an imminent security risk – even though there are no restrictions on how long hair on the head can be.

That argument didn’t impress the high court; according to the legal news outlet SCOTUSblog, Justice Samuel Alito joked that prison guards could comb Holt’s beard “to see if a SIM card – or a revolver – falls out.”

The case, Holt v. Hobbs, still awaits the Supreme Court’s verdict. But the problem of uneven religious accommodations and other First Amendment violations that predominately affect prisoners isn’t restricted to Holt, or to the state of Arkansas. Instead, some advocates say, it’s a widespread problem that affects many religious minorities.

Gurjot Kaur, senior staff attorney at the Sikh Coalition, told Church & State that Sikh men, who grow beards and leave their hair uncut for religious purposes, are often unable to exercise their religious freedom rights while incarcerated. Kaur cited mandatory shave policies in prisons as an example of barriers to true religious freedom for Sikhs.

According to Kaur, the Sikh Coalition was forced to intervene on behalf of a California Sikh who, while serving an extended prison sentence, was unable to follow his faith’s grooming practices.

“He wouldn’t be allowed to take certain classes and was deducted points, which added to his general sentence,” Kaur explained. California’s statute was eventually repealed, but mandatory shave policies for prisons are still on the books in other states.

These restrictions on grooming are also present in the armed forces and in some municipal police and fire departments, which creates yet another challenge for religious minorities. The Pentagon recently announced adjustments to its grooming policies that would exempt certain members from its required full shave and boot camp buzz cut. But according to Kaur, the reforms haven’t meant much in practice.

“We haven’t seen anyone successfully accommodated,” she said. Lack of reasonable accommodations, advocates say, could deter religious minorities from entering the armed services, thus adding to their social marginalization.

But there’s more to contemporary religious persecution than debates over beards. Visible religious minorities also experience zoning discrimination, as city councils sometimes unfairly reject permit requests for constructing houses of worship. 

All religious groups can encounter zoning issues, but members of minority faiths face special challenges in this area. Sometimes, it’s rank and open bigotry.

Consider the Kennesaw mosque. Late last year, the Suffa Dawat congregation in Kennesaw, Ga., requested a zoning permit to build a worship center in a local strip mall. Although the city council had recently voted to approve a similar permit for a Protestant church, it overwhelmingly rejected a permit for the mosque. Local activists testified against the mosque’s construction at a public hearing. Some argued that Muslims didn’t merit First Amendment protections.

“We have heard so many bad things about the Islamic religion, about Shariah law and you see it on TV, and we’re scared of you. I’ll tell you I’m scared to death of you,” one resident said.

Kennesaw’s Muslims retained legal counsel, and the city council swiftly reversed course in a move that infuriated activists but prevented a legal battle that experts theorized they’d likely lose. Of note: Kennesaw was only the latest Georgia municipality to deny a zoning permit for a mosque. The towns of Alpharetta and Lilburn recently lost legal battles for doing the same – courtesy of Suffa Dawat’s attorney.

This phenomenon isn’t limited to Muslims; according to the Sikh Coalition’s Kaur, Sikhs are also affected by anti-Muslim prejudice, primarily because of the turbans worn by Sikh men and some women.

“After 9/11, Sikhs have been conflated with al-Qaida, the Taliban and with ISIS,” the attorney said. “There are no positive images of Sikhs, or messages explaining [the turban’s] significance – like equality and fighting for justice.”

In some cases, Sikhs have even been murdered. On Sept. 15, 2001, Balbir Singh Sodhi was gunned down outside the Mesa, Ariz., gas station he owned. The killer, Frank Silva Roque, shot Sodhi five times. He later told police he believed Bodhi was a Muslim. Roque was found guilty of first-degree murder and is currently in prison.

Stories like this are tragic, but Kaur says there is room for optimism. She noted that rates of hate crimes against Sikhs, at least, are down, and she credits legal action with an improved religi­ous liberty outlook for the community.

The latter tactic – legal action taken to protect the constitutional rights of all Americans, regardless of religious affiliation – is also one endorsed by Americans United. The religious liberty watchdog filed a friend of the court brief in Holt v. Hobbs, and regularly pursues litigation on behalf of other belief minorities, including non-believers, Pagans, Wiccans and others.