It might be brilliant, but it would be repulsive to most people not named Manson or Hussein. And the better and more effective the movie, the more people would hate it, because Nazism is scary enough with the ugly face of illiterate and lunatic skinheads, but imagine how scary it would be if Hitler had been as sympathetic as Tom Selleck, and Goebbels as emotionally manipulative as Spielberg. I've made a very extreme example to illustrate that Cider House Rules has a similar, if somewhat less dramatic, situation. Although there are some arguments on both sides, the movie has a fundamentally pro-choice stance on abortion, and some people find that morally repugnant. It has a father who commits incest with his daughter, and although he does great harm, he is not portrayed as an evil person.
Some people find that morally repugnant.
But these are not really weaknesses in the film. They are, in fact, strengths. The movie delivers its message powerfully, whether we agree or not. Strange one, this. Charlize's nude scene was cut from the length of the original theatrical release.