to same sex couples getting married, which was found to be impermissible discrimination. Just your example is supposedly based on "business" concerns and the other on the baker's principles. In reality I think the discrimination against BYU would in fact be principles-based, because people think their principles are better than our principles.
We are in fact getting dangerously close to being in a place where not only will individuals' intolerance begin to affect us, but freedom of religion will be infringed, if we're not there already, by our state and federal governments. There's a reason the church has focused on this recently, and the problem isn't getting better.