Interesting... customer interactions aside (the difficulty of the customer is probably irrelevant to the case), it didn't come off that way from the New York Times article, but it did in the official opinion from the Colorado Court of Appeals (
https://www.aclu.org/legal-document/craig-v-masterpiece-opin...). Might not change the scope for a narrow ruling, of course, but depending on the "scope" this might affect the outcome.
It's worth noting that religion per se is not a protected class in Colorado's discrimination laws. Sexual orientation is. (https://law.justia.com/codes/colorado/2016/title-24/principa...)
Even if religion was a protected class, one problem I see here is that it really isn't "Christianity" as a whole in the Bible verse case that the owner found distasteful per se. Rather, it's the opinion expressed by the Biblical verse chosen. Christianity encompasses a wide range of opinions, after all. There are some Christians who downplay the anti-homosexual verses in the Bible (or have different interpretations to them, eg, they believe there is some degree of mis-translation). If the baker had refused to make a cake with a more universal symbol representing Christianity as a generic concept (say a cross), I think there's a stronger case that this is religious discrimination.
But as it is, it's a message. Compare this to if the reference was non-Biblical but similar in intent. Say, the customer wanted to write a message like "ALL FAGGOTS WILL BURN IN HELL" on the cake (weird message for a cake, but so is an anti-homosexual Bible verse IMHO :) ). The owner certainly has the right to refuse here because they find the message distasteful. Is there much of a difference? Whereas, in the other case, it involved a class of people that the owner found distasteful, yet was protected by the law above.
I will say that it is indeed these sort of cases that do make "protection laws" a bit troublesome... such codes force the baker to go against his or her own personal beliefs. If it's just one cake baker losing business over a moral code like this, it's probably better to err on the side of not worrying about it. The trouble is, we're well aware of the results that happened when a minority group isn't protected, and suppression of the minority group is systematic and widespread. In other words, from my vantage point, the alternative appears to be worse.