NPR's reporting of the same case says the following:
Writing for the case, Justice Anthony Kennedy said that while it is unexceptional that Colorado law "can protect gay persons in acquiring products and services on the same terms and conditions that are offered to other members of the public, the law must be applied in a manner that is neutral toward religion."
He said that in this case the Colorado baker, Jack Phillips, understandably had difficulty in knowing where to draw the line because the state law at the time afforded store keepers some latitude to decline creating specific messages they considered offensive. Kennedy pointed to the Colorado commission's decision allowing a different baker to refuse to put an anti-gay message on a cake.
. . .
"The outcome of cases like this in other circumstances must await further elaboration in the courts, all in the context of recognizing that these disputes must be resolved with tolerance, without undue respect to sincere religious beliefs, and without subjecting gay persons to indignities when they seek goods and services in an open market," Kennedy said.
The bolded text in particular is some spicy meatballs. Also, the baker was previously recorded saying: "I'm just trying to preserve my right as an artist to decide which artistic endeavors I'm going to do and which ones I'm not."
If anything, the Supreme Court overturning the lower court's ruling preserves the rights of every business owner to not go against their own particular morals. If religious businesses would be forced to provide services for LGBT events and organizations, then LGBT-friendly businesses would be forced to provide for anti-LGBT events and organizations.