What I read was that coffee may have some beneficial effects. The study, such as it was, showed lower amounts of cirrhosis of the liver among coffee drinkers. Of course, what I read said nothing about how much alcohol the coffee drinkers drank compared to the non-coffee drinkers, and there are other unanswered questions as well.
I think it's more an issue of the news producers hyping the study without giving out all the information. From what I could read into it, the study itself did not pretend to prove anything, it just pointed out a possible connection that they might study more. It's the news media, however, who turns it into, "Coffee Cures Cirrhosis!"