The sudden national emphasis on transgender rights has spurred legal battles, boycotts and a spate of newly minted pronouns -- a controversy critics say is out of kilter for an issue that directly affects about two in every 1,000 Americans.

“Activists are now pushing aside family values, parental rights, indisputable science, the best interests of children, religious freedom, free speech, property rights, and local control in order to aggressively push the transsexual, cross-dressing, ‘sex change’ agenda,” said Randy Thomasson, president of SaveCalifornia.com, a Golden State organization that bills itself as pro-child and pro-family. “[They] have coordinated to push this new ‘project’ to keep their funding coming.”

Critics say they don’t want men using women’s restrooms and are even more adamant that they don’t want biological boys permitted to share restrooms and showers with girls in public schools.

Last month, the Obama administration announced a new directive that every public school in the nation must provide transgender access or face the loss of federal funds. The directive came as North Carolina passed a law banning individuals from using public bathrooms that do not correspond with the biological sex listed on their birth certificates.

Also last month, Texas and 10 other states declared they would defy the federal directive and sued the Obama administration over it.

"He's trying to cram down as many parts of his liberal agenda on the United States of America as he possibly can," Texas Gov. Gregg Abbott said.

Even if the issue requires policy changes, White House involvement has precluded state and local governments from building consensus and crafting real solutions, wrote Rob Port, founder of the North Dakota political website sayanythingblog.com.

"How are local officials supposed to deal with this issue when the president of the United States is busy — for transparently partisan political reasons — sticking his nose into it?" Port recently wrote.

The transgender rights debate has extended well beyond the bathroom. Colleges and universities have banned the use of certain pronouns that they believe can exclude transgender men and women. New York City has passed a law that would penalize employers and landlords who refuse to address their workers or tenants with the pronoun of their choosing – including the “gender-free” pronouns “ze” and “hir.”  

Such laws force people who, whether for religious or scientific reasons, may not see gender as a fluid concept to go against their beliefs, said UCLA School of Law Professor Eugene Volokh, a free speech and religious freedom expert who writes a blog for the Washington Post.

“It requires people to essentially make political statements that they don’t want to make, as the use of ‘ze,’ for instance,” Volokh said. “It requires people to say things that they may sincerely believe are lies and that indeed are contrary to what they see as God’s ordering of the world.”

The New York City law was enacted in December, but to date, no one has been cited for violating it, officials told FoxNews.com.

“We have not fined any employers, landlords, or providers of public accommodations for misusing a transgender person’s preferred pronoun,” an official said to FoxNews.com.

After national retail giant Target announced that customers would be able to use the restroom of their gender identification in a statement responding to North Carolina’s “bathroom bill,” the American Family Association launched a petition that has so far gathered 1.3 million signatures from people pledging to boycott the chain. The critics have claimed credit for a 20 percent decline in the company’s market capitalization, although economists point to a combination of factors.

College students and faculty have embraced transgender rights. Last week, Yale University announced that each of its 23 buildings on campus will have gender-neutral bathrooms, one of several changes made this past year to make the school more transgender friendly.

"Yale aims to be a leader on this front," Tamar Gendler, dean of Yale's Faculty of Arts and Sciences, said. "Part of what is important about the all-gender bathroom project and about putting it at the top of our commencement site, is this is about public signaling."

Professors are now using preferred pronouns when addressing students, and the school is allowing transgender students to change their names on their school identification card and the school's web portal at no charge.

The University of Vermont last year also began officially addressing transgender students using the name and gender pronoun of their choice. Smith College, an all-women's school in Massachusetts, made headlines last year when it began admitting students who were born male but identify as female.

Harvard allows housing based on the gender with which a student identifies for sophomores, juniors and seniors and allows students to use the bathrooms with which they feel most comfortable. But it does not allow non-legal names to appear on official documents.

Proponents applaud the Obama administration and reject the idea that a small minority of transgender women and men should drive large-scale legal and social changes.

“Civil Rights laws were never meant for the majority, they were created for the minority,” Mara Keisling, executive director of the National Center of Transgender Equality, told FoxNews.com. “We have all sorts of laws aimed at things that are low population.

“We don’t say that small Indian tribes shouldn’t be honored and respected,” she adds. “Those of Jewish faith is a low part of the population, but nobody says let’s not protect the Jews. It’s an unsettling thing that this is occurring with transgender issues.”

Perry Chiaramonte is a reporter for FoxNews.com. Follow him on Twitter at @perrych