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)
Audio problem: In Maroon's office, when he says to Valiant "I want you to get me a couple of pictures to wise up the Rabbit with," notice the next shot is of Maroon from the back of his head. Notice his mouth doesn't match the words he is saying. (00:06:30)
Revealing mistake: When Judge Doom knocks Eddie off the Dip machine, note the Acme Curve Ball boxes in the background that appear to be written backwards, revealing a flipped shot. (01:26:30)
Continuity mistake: After Roger springs onscreen from an underground pipeline at the Acme Factory, a steel grate is thrust high into the air, falling right in front of Judge Doom (however the shot cuts away half a second before it's supposed to hit the floor). But two shots later that same grate is seen falling from a much higher elevation again. It should have been lying on the floor at this point. (01:21:10)
Revealing mistake: When Daffy gets thrown into Donald's grand piano, a wire is visible on the upper left side of the screen - closing the lid on his beak. (00:15:40)
Visible crew/equipment: A crew member's hand is visible turning the steering wheel of Eddie's beat-up Plymouth when Roger skids it to a halt. (01:17:35)
Revealing mistake: During the piano duel finale, Donald blasts a cannon at Daffy and the grand piano collapses - seemingly from the impact. But if you look closely there are actually ropes pulling the piano's legs from somewhere offstage. (00:17:05)
Visible crew/equipment: Set lights are visible on the ceiling for a few shots in the scene where Eddie and Baby Herman are discussing Marvin Acme's will. (00:34:30)
Continuity mistake: When Benny the Cab approaches a bridge where the woman is pushing her baby carriage, the sun casts shadows at wildly different angles in alternating shots. (00:59:30)
Revealing mistake: When Eddie and Roger are using Benny the Cab to run from the weasels, Eddie reverses gears and backs into the alley. It may be Benny the Cab's image onscreen, but a shadow on the ground actually reveals the go-cart which Eddie uses for the take. (00:58:40)
Visible crew/equipment: When Eddie grabs a newspaper from Baby Herman, you can briefly see the mechanical arm used to hold it - sticking out of the carriage for a split second. (00:35:00)
Revealing mistake: After Lena Hyena plants a kiss on Eddie, he tumbles down the street and lands face-first onto a solid white line. Pavement is animated into this shot, however a reflection of the stage floor is still visible. (01:13:20)
Revealing mistake: As Roger gets ready to take a drink of bourbon in R.K. Maroon's office you can see a moving shadow on the desktop - which is that of a mechanical arm used to hold the shot glass. (00:23:40)
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)
Visible crew/equipment: In one shot where Eddie leaps into a wall of pogo stick boxes at the Acme factory, a springboard used for the stunt is partially visible behind the red banana skin containers. (01:24:35)
Revealing mistake: At one point where Roger drags Eddie over to the electrical outlet spy hole in Dolores' secret room, Roger says "This will be a great place to hide." Both of them are handcuffed together in this shot, but Roger's shadow is not animated into his cuff. (00:44:20)
Revealing mistake: After being flattened by the steamroller, Judge Doom staggers over to the compressed air tank and reinflates himself. When his black hat pops off, strings can be seen pulling it up. (01:29:45)
Revealing mistake: When Benny the Cab jumps onto a bridge with Roger and Eddie, a red Ford De Luxe skids to avoid a collision. Notice how tire tracks from a previous take are visible on the pavement. (00:59:35)
Revealing mistake: After Bongo the Gorilla Bouncer tosses Eddie into a pile of garbage cans in the back alley, Eddie lifts himself up and here we can see that he's wearing knee pads beneath his pants. (00:21:25)
Revealing mistake: After Roger reads Marvin Acme's will out loud, all of the toons start jumping for joy. Meanwhile the music machine is still activated in the background, and its colorful flashing lights are being reflected on the ground near Betty Boop and Tweety at the front of the crowd. With all of the toons grouped together like they are, the machine's colorful lights should have been obscured, not reflected. (01:35:30)
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.