A 7-2 win at the Supreme Court is a big deal. But some advocates of religious freedom minimized the importance of Masterpiece Cakeshop v. Colorado Civil Rights Commission, saying it was a narrow ruling that applies only to the manifest hostility to religion the commission showed in adjudicating Jack Phillips’s case. Religious-liberty opponents have claimed the decision is an open door to invidious discrimination, including racism. Both views are wrong.

The hostility to Mr. Phillips and his beliefs isn’t unusual. The rhetoric Justice Anthony Kennedy condemned—and cited as examples of constitutionally impermissible animus—is often heard from antagonists who attempt to ruin religious believers. Comparisons to racism and Nazism such as the Colorado commission made are standard for left-liberal culture warriors.

In 2016 the chairman of the U.S. Civil Rights Commission wrote—in an official report—that “ ‘religious liberty’ and ‘religious freedom’ . . . remain code words for discrimination, intolerance, racism, sexism, homophobia, Islamophobia, Christian supremacy or any form of intolerance.”

The following year Rolling Stone magazine published a friendly profileof Tim Gill, “the Megadonor Behind the LGBTQ Rights Movement.” Mr. Gill is bankrolling the effort to pass new antidiscrimination laws that treat “sexual orientation and gender identity” as a protected class like race. He revealed why gay-rights activists oppose religious-liberty claims with such vehemence: “We’re going to punish the wicked.” The Colorado Civil Rights Commission’s extreme and open bias is consistent with a campaign to punish heretics. But antidiscrimination policy is supposed to be a shield. It has been transformed into a sword, used to coerce people into affirming a sexual orthodoxy.

Consider Philadelphia, whose local government recently announced it would no longer work with Catholic Social Services on foster care. That effectively closes Catholic foster care in the city, because the government has ultimate responsibility for children in need. If the government won’t work with a foster agency, that agency can’t help children.

Why did Philadelphia do this? Not because the Catholics do a bad job: the city ranked Catholic Social Services as the second-best foster-care agency of the 28 it worked with. The sole reason is that the Catholic agency doesn’t place children with same-sex couples.

Catholic Social Services has never received a complaint from a same-sex couple wanting to foster a child. Same-sex couples could foster or adopt a child from another agency. Yet Philadelphia officials were willing to shut down a good agency that causes no harm merely to send a message that its religious beliefs are intolerable—precisely what the Supreme Court in Masterpiece Cakeshop said the government may not do.

Catholic agencies decline to place children with same-sex couples not for reasons of sexual orientation, but because, as Pope Francis has said, “Children have a right to grow up in a family with a father and a mother.” The issue isn’t whether gay people can love or care for children—of course they can—but in the church’s view, the two best dads in the world cannot make up for a missing mom, and vice versa.

If those playing down the importance of the Masterpiece Cakeshopruling are wrong, those overstating it are also off base. “Family Guy” creator Seth MacFarlane claimed that “it’s a shorter walk than we think, particularly today, from ‘I won’t bake them a cake because they’re gay’ to ‘I won’t seat him here because he’s black.’ ” This wildly mischaracterizes Mr. Phillips’s position. The Masterpiece proprietor serves all customers, regardless of sexual orientation, but he can’t in good conscience communicate all messages or celebrate all events. He is motivated by his Christian belief that marriage unites husband and wife, not his customer’s identity.

This disagreement about the definition of marriage occurs among people of good faith motivated by honorable theological and philosophical premises, as Justice Kennedy recognized in Obergefell v. Hodges, the 2015 same-sex-marriage decision. And as he wrote in Masterpiece, “religious and philosophical objections to gay marriage are protected views and in some instances protected forms of expression.”

That is why states should be careful not to abuse antidiscrimination policy in a way that amounts to an enforcement of an orthodoxy regarding questions about sex on which reasonable people can disagree.

Monday’s ruling won’t open the floodgates to invidious discrimination as critics imagine. But neither should we gainsay its wider applicability. The Supreme Court has said clearly that the government may not punish people because of their religious beliefs. Any generally applicable, neutral law must serve the common good, not punish those whom people in power deem to be “wicked.”