I know that if I were CEO of a corporation (read: a machine that produces money) and my product was regularly rejected over a competitors product line which was always overwhelmingly successful (Mel Gibson), then I would try to figure out what made the other product better in the eyes of the public. I would make some kind of effort to make a similar or better product...
But then again, what do I know? No one pays me tens of millions a year to oversee movie production...
Certainly genuine politics is a factor. "Office politices" also plays a role (investors beware).
When a studio buys out another studio, some projects have already been given the greenlight and contracts are inked, etc. Some people don't like some other people (and this can be producers, not just actors/writers/directors). Sometimes it is someone who doesn't like a genre of movie.
Personal grudges and vendettas will come into play to sink someone's film from within the company.
Even when a smaller film succeeds, it can end up being a "loss" for the studio by being made to shoulder some of the written down expense for another film (say someone else's pet project bombed; if he's a favored staffer, his loss may be written down under someone else's film).
All of this sounds like cooking the books (the original Batman didn't produce a "profit" even though it took in over a quarter of a billion dollars; just so happened that the screenwriter was to see share of the "profit" which never materialized).
Hollywood is into vanity. Some will cut off their nose to spite their face. If they were interested in running it as a "business", they would support films that the public is supporting. They'd rather be tastemakers pushing their own agendas and attempting to squash dissent.