I agree, it should be a blanket law, but if the B&B also refused to allow an unmarried straight couple to share a room then it wouldn't be discrimination. The fact that in this instance the couple happened to be gay actually has no relevance to the situation.
Do we know that the B&B hasn't turned away unmarried straight couples in the past?
The issue is that the couple were gay and in a civil union which is treated in most repsects like a marriage. So the B&B were effectively discriminating against them because of their sexuality not their married status. The ruling could have gone the other way if the couple had not been in a civil union.