When it comes to endings, the brighter ones tend to be more popular than its opposition. This can be semantically misinterpreted as a "good" ending and more than likely, be the only kind of ending that people crave for in a story. Well, sometimes the more appropriate ending would be on a sadder or even unhappy kind just to fit the flow, instead of shoehorning some kind of happy ending.
Some recent examples of this, in my opinion, were Mirai Nikki and Tasogare Otome x Amnesia. I wont give any spoiler to either of them, so I'll just say they both could of ended perfect a few seconds before the deliberate insertion of a few seconds to indicate everything was happy. I haven't seen their manga so maybe the endings are the same or even different, but the anime version ending felt too cheap.
With that said, there are times when you I can say a happy ending is appropriate, good example is Rainbow: Nisha Rokubou no Shichinin. I watched Rainbow when it first aired and the ending was well fit for such a dark anime.
I think that people need to recognize the nuances of story telling and realize that stories aren't aways going to end in a "Happily Ever After". When there is a non-happy ending it doesn't mean it was a bad ending. You have analyze the full anime and assess how this actually ask yourself if it fits into the story.
I've heard in some case, people would say that the overall story become useless when it ends unhappily. These kinds of opinions seem sad to me, because they will never appreciate those different kinds of anime where its not really about everything being something cheerful. Rather it was try to go for something deep or just to cause some kind of reaction in the viewer.
Don't buy the hype, ending that are happy shouldn't be the only qualified ending for an anime, or even any story medium. We have to get over the knee-jerk reaction to non-traditional ending and just give them a chance. Let it sit in your mind for a bit and maybe think of how you would feel if they concluded the story with an opposite perspective. All I'm asking for is a proper ending that wraps up the storyline and at least make it feel a little right.