Continuity mistake: Before Eddie grabs Roger to toss him out of the apartment, a blanket hung over the edge of the pull down bed rearranges itself between shots. (00:37:25)
Visible crew/equipment: When Eddie tries throwing Roger out the door, Roger explains that he's being framed by somebody. Here, notice the film crew's power supply cords running along the floor from the hallway into Eddie's apartment. (00:37:45)
Continuity mistake: In the scene at Valiant' office, Roger starts reading the letter but when he jumps off the bed in front of Valiant, the letter disappears. (00:38:35)
Revealing mistake: When Roger is bouncing on Eddie's bed, the landings are not in time with Roger's feet. (00:38:45)
Audio problem: In Valiant' office after Roger reads the letter and Valiant says, "Why didn't you just leave the letter there." Notice Roger standing on the bed, you hear him talking, but his mouth doesn't move. (00:38:45)
Revealing mistake: When the weasels are at Eddie's apartment and Roger is handcuffed to Eddie, Roger runs under the bed and drags Eddie on the floor. As he pulls him you can clearly see a board with wheels under Eddie that is pulling him under the bed. (00:38:50)
Continuity mistake: In Valiant' office notice the whiskey bottle to the right of Valiant. Then Roger is about to sit in his brother's chair. While Valiant is yelling at him, look right in front of him the whiskey bottle is there, but then when he sits down the bottle is back at its original spot. (00:39:15)
Continuity mistake: In the scene where Hoskins says, "I'm calling the cops," his eyes are following Roger as he walks across the desk, but when you see Roger he is still standing near the chair. (00:39:30)
Revealing mistake: After Eddie tells Roger that his handcuff keys are missing, they leap over the bed as the Toon Patrol sirens approach. When Eddie lands on the floor, his bedsheets get disturbed by a large blast of air - most likely the backfire of a safety cushion that was hidden behind the desk to break his fall. (00:40:10)
Revealing mistake: In the shot where Roger looks out of Eddie's apartment window to see the weasels approaching, you can see how their animations overlap the window sill as they cross the street. (00:40:20)
Audio problem: When the Toon Patrol shows up at Eddie's door in search of Roger, they start knocking and the door shakes in response, but sometimes no sound can be heard to correspond with the door's movement as they knock. (00:40:45)
Revealing mistake: After shooting their way into Eddie's apartment, the weasels start walking in and cast long shadows on the floor. But the only shadow visible in a reflection on the nearby glass doors is that of Wheezy's Tommy gun. (00:41:10)
Continuity mistake: When Eddie is at the kitchen sink pretending to do laundry, Smart Guy pulls up a chair and starts asking about Roger's whereabouts. Eddie is squeezing a black sock with his right hand, but between shots he submerges it in the water. (00:41:40)
Revealing mistake: A string is visible suspending Greasy's gun when Smart Guy orders everybody to search Eddie's apartment for Roger. (00:41:55)
Continuity mistake: In the scene where Hoskins is washing his clothes and hiding Roger notice that the weasel talking is holding a gun. Hoskins puts a bar of soap in his mouth and the gun disappears. Then when he comes back to Hoskins the gun reappears. (00:42:15)
Other mistake: Three shots after Eddie stuffs the soap into Smart Guy's mouth, when the other four weasels notice him tumbling down the stairs, a chair can be seen flying across the room. This is impossible, because the other four weasels are together, and Smart Guy was talking with Eddie, so there was nobody to throw the chair. (00:42:15)
Revealing mistake: After getting a mouthful of soap from Eddie, Smart Guy is thrown across the room and loses his gun. When the gun hits the wall you can see it dangling from a puppeteer's string in mid-air. (00:42:15)
Revealing mistake: When Wheezy and Psycho laugh at Smart Guy after he has fallen down the stairs, if you look closely you can see the wires holding Wheezy's machine gun up. (00:42:20)
Continuity mistake: In the scene where the weasels are in Eddie's office, when the other four weasels see their leader falling down the stairs, Stupid (the fat weasel) closes the middle drawer on the filing cabinet. In the next shot the drawer is open. (00:42:20)
Revealing mistake: When a bar of soap knocks Wheezy into the window blinds, he casts no shadow on the wall, but his Tommy gun does. (00:42:30)
Answer: There's really a lot of possible reasons he hates other toons. There's a whole Roger Rabbit book and comic book series that explain Doom's background more. In the film, he's greedy and wants to destroy Toon Town to build the freeway to make more money. In human disguise he's also seen as merciless and is just punishing toons to maintain law and order, etc. Although that's just an excuse to kill toons as well. However, not explained in the film; as a toon he was cast as the antagonist in cartoon films until an accident one day left him thinking he was an actual villain (as opposed to just an actor playing one). That's when he began his life of crime, including killing Teddy Valiant. So his hatred of toons is more about him being evil and not a personal vendetta against them, like Blade's motives.