Well, it is a stop-motion movie with a somewhat dark content. Another stop-motion movie in that regard was Frankenweenie. The studios came to the conclusion that if a stop motion movie did not do it as good as expected, it would not be worth the risk (it probably never occurred to them the fact that it was black and white could have had something to do with it):
http://www.cartoonbrew.com/animators/did-frankenweenie-kill-guillermo- del-toros-stop-mo-pinocchio-project-77266.html
That's like assuming if a CGI movie did not do it well enough, one should be more careful with other CGI movies as well. But that's how Hollywood works:
Most greenlight decisions in Hollywood are reached in part based on computer programs that analyze how similar releases have performed in the past.
http://articles.latimes.com/2012/nov/19/entertainment/la-et-ct-life-of -pi-tough-sell-20121119/2