I think that there is something to be said for large publishers, but I 100% agree that they're motivated by dollar figures. (Which makes sense, they are businesses!) If something is seen as both good and commercial, they'll publish it. But if they think that your story has too small of a market (true for a lot of genres/novels/whatever), they won't touch you. It's a rational business decision, even if it does leave out some otherwise good stories.

I do think that you can carve out a niche through indies, although it's hard to do, and probably relies as much upon business sense/marketing as it does through good writing ability. (I think that both are probably rather necessary to create a successful indie book.) I've seen a few good posts on how authors have managed, but probably even they got lucky!