Joe said it as succinctly as anyone can.
'A business ain't a human'...an 'American' human with COTUS rights.
It's an enterprise....conducted by humans to be sure, but there is a nuance there, a delineation that must be observed.
As a public 'enterprise' his is obligated to follow the laws of the land....specific to such enterprises. And the court so ruled.
But, as you said, businesses are run by people, and as such people have the right to their religious freedom.
I’ve argued that a business is run by the employees, and I think Phillips is the only employee of his shop, or at least the only baker, so asking his business to make the cake means that he has to violate his cotus rights and religious views to make the cake.