Reading his explanation on Facebook, I think it makes sense. Of course CNN is making hay out of this, but I don't see any real issue here.
Yeah, sure, and it just so happens that he's following the flag code now, when I'm willing to bet he wasn't 100% consistent with it before. I doubt anybody responsible for the flag going at half-mast or not does. In fact, haven't flags across the nation gone to half-mast for other massacres that didn't involve government officials? Not counting San Bernadino in this case, since it was specifically mentioned in the article.
Heck, flags in Utah have gone at half-mast for the death of a top Mormon church leader or his wife more than once before.