Yes, we really put "Race" as a theme in Roger Rabbit. And no, not because one of the major live-action-meets-animation films that preceded this one is the racist Disney flick Song of the South. (Source)
We admit it's a bit of stretch—and not because Toons can stretch themselves into any shape they want—to call Roger Rabbit a racial allegory of any kind, but there are parallels to be drawn between the divided neighborhoods of humans and Toons in this film and the divided neighborhoods between people of different racial backgrounds today.
Questions About Race
What is the general attitude humans have toward Toons?
Are Toons considered second-class citizens?
How is Eddie's attitude toward Toons similar to racist attitudes some people harbor today?
Chew on This
Toons are marginalized and many people don't care if they're wiped out. They need Eddie as an ally to protect them and to help change attitudes toward them.
The divide between Toontown and the rest of L.A. is direct commentary on racially divided cities today.