He sells custom decorated wedding cakes. If your position is the couple have a sex right to buy their wedding cake and the baker has a religious right to not compromise his religious beliefs then how do we resolve it?(this isn't true legally obviously, owner and customer have different legal burdens, so this is just a hypothetical) Whose right trumps who? Not making the cake sides with the owner, making the cake sides with the couple. Any outcome violates someone's rights.
No, you misunderstand what is the issue.
If two gay guys walk in to Wendy's with their shirts off, and the manager denies them service, they don't get to say he is violating their rights.
The issue there is not that they are gay, but that they have their shirts off. Similarly, the issue is not that they are gay, but are requesting a "gay" cake. It's not their protected class at issue, but the service. It is decidedly illiberal to force the baker to bake that cake.