The message conflicted with their beliefs related to their religion, as opposed to simply being anti homosexual due to your everyday bigotry (unlike the example made regarding black people wanting a cake - as far as I know there is no religious base for being against a black couple, also there is a difference between a cake simply showing a happy couple and having a message of support for something).
The message was against their Philosophical Beliefs so they refused to do it. They have been punished for it. In this case the Equality Law protecting them and their Philosophical Beliefs were trumped by the Equality Law protecting homosexuals from discrimination.
Now, is this purely because of the whole business aspect of the Law and therefore their business should be 'Agnostic' so Beliefs have nothing to do with it. Or, because they are willing to serve homosexuals, but like with all customers reserve the right to refuse designs they have issue with, is the Equality Law unjustly trumping one person for another?