Judge Doom was actually a corrupt judge who was secretly working with a real estate developer named Mr. R.K. Maroon. They wanted to tear down Toontown and build a new highway in its place, and they believed that Roger Rabbit's murder would create an environment of fear and chaos that would force the toons to leave.
Judge Doom planted evidence at the scene of the crime and manipulated the investigation to make it look like Roger was guilty. However, the real culprit was revealed to be Judge Doom himself, who was ultimately killed by his own concoction, "Dip," which dissolved him into a pile of goo.