Is "The Cabin In The Woods" really meant to be a metaphor for the horror genre?

The very short answer is yes and no. The film was clearly intended as a comedy-based deconstruction of the horror genre, but the makers were also quite careful not to fall into the trap of simply making a straight parody (a la 'Scary Movie' or 'Tucker & Dale Vs. Evil').

Filmmaker: So far we’ve been talking about Cabin as strictly a horror movie, but it’s also got some very strong comedic elements. Was it difficult to balance those two genres?

Goddard: It was the hardest part of the job – maintaining that tone. Because we do both, we go from horror to comedy and comedy to horror. And you have to be really careful with that, because with comedy it would have been very easy to veer too far into parody. And if you go the other way, suddenly you’re becoming that which you’re commenting on. And so we really had to walk the line.

In terms of balancing the tone, I found what it usually came down to was my gut reaction. There’s no way to completely intellectualize it. I just had to think about each scene and say, “Okay, we’ve gone too far here, let’s dial it back,” or, ‘this is a good place where we could take things a little further.” You just have to trust your gut as you go. - _{^{A Conversation with Cabin in the Woods Director Drew Goddard}}

I think it's pretty clear that it's a horror movie about horror movies. For example, in the interview quoted by @user7812, Goddard says, "I wanted it to be a movie about the genre..."

Also, in an Onion AV Club interview with Whedon, Whedon describes the Sitterson and Hadley characters as screenwriters like Whedon and Goddard: those characters are crafting their own horror movie inside the movie.