The baker in question specializes in weddings. They may refuse customers if the function at issue is not a wedding. The baker considers the formalized celebratory union of anyone other than a man + woman to be not a wedding.
Now, based on no legislation (as one dissenting Justice makes scathingly clear), a new "protected class" has been created. The baker still considers a pair entering that "protected class" not a "wedding", a view the ruling notes still should be respected and free to hold & act on.