In Roger Rabbit, the line separating cartoon artifice and the real world is crossed repeatedly, and suddenly the rules of both worlds are forced to coexist. Now Roger Rabbit getting whacked in the head (stars, birds) isn't nearly as funny. Toons are abused in the real world for the entertainment of humans. And when Eddie Valiant ventures into Toontown, what happens? After a cheery greeting, he crashes his car, is stalked by a crazed woman and becomes the butt of a cruel joke at the hands of Bugs Bunny and Mickey Mouse. Funny in a cartoon world, maybe, but not when the victim is a real person.
I remember reading an article around the time Roger Rabbit came out. The writer was very critical of the movie, likening Toontown to the experience of black entertainers in the 1930s and '40s (segregated, abused by the Hollywood establishment, tolerated only as long as they entertained white audiences). While I'm certain it wasn't the intent of the filmmakers to portray Toontown this way, the fact that an effective racist analogy could even be made is one more reason I dislike the movie.
Who Framed Roger Rabbit is a fine technical achievement, but the meanness and cruelty of the story does it in.