"It is time — past time — to make plain that, while the pandemic poses many grave challenges, there is no world in which the Constitution tolerates color-coded executive edicts that reopen liquor stores and bike shops but shutter churches, synagogues and mosques."

Wrote Justice Neil M. Gorsuch, in his concurring opinion, quoted in "Splitting 5 to 4, Supreme Court Backs Religious Challenge to Cuomo’s Virus Shutdown Order/Justice Amy Coney Barrett played a decisive role in the decision, which took the opposite approach of earlier court rulings related to coronavirus restrictions in California and Nevada" (NYT).

It was 5 to 4, not 6 to 3, because Chief Justice Roberts voted with the liberal members of the Court. He wrote: “Numerical capacity limits of 10 and 25 people, depending on the applicable zone, do seem unduly restrictive... It is not necessary, however, for us to rule on that serious and difficult question at this time. The governor might reinstate the restrictions. But he also might not. And it is a significant matter to override determinations made by public health officials concerning what is necessary for public safety in the midst of a deadly pandemic. If the governor does reinstate the numerical restrictions the applicants can return to this court, and we could act quickly on their renewed applications."

Unlike Roberts, Justice Sonia Sotomayor, joined by Justice Elena Kagan, reached the substance of the claim and found  no violation of rights:  “States may not discriminate against religious institutions, even when faced with a crisis as deadly as this one. But those principles are not at stake today. The Constitution does not forbid states from responding to public health crises through regulations that treat religious institutions equally or more favorably than comparable secular institutions, particularly when those regulations save lives.” 

That is, no one is saying that the government can discriminate between religion and nonreligion. It must treat comparable activities the same, but the question is what is comparable. They're disagreeing about whether religious services are like stores. That's what the parties were arguing about:

[L]awyers for the diocese argued that its “spacious churches” were safer than many “secular businesses that can open without restrictions, such as pet stores and broker’s offices and banks and bodegas.” An hourlong Mass, the diocese’s brief said, is “shorter than many trips to a supermarket or big-box store, not to mention a 9-to-5 job.” 

Ms. Underwood responded that religious services pose special risks. “There is a documented history of religious gatherings serving as Covid-19 superspreader events,” she wrote. Indoor religious services, Ms. Underwood wrote, “tend to involve large numbers of people from different households arriving simultaneously; congregating as an audience for an extended period of time to talk, sing or chant; and then leaving simultaneously — as well as the possibility that participants will mingle in close proximity throughout.” Still, she wrote, religious services are subject to fewer restrictions than comparable secular ones. “Among other things, in both red and orange zones, casinos, bowling alleys, arcades, movie theaters and fitness centers are closed completely,” she wrote.