You have to remember that Roger Rabbit was made when no one had any interest in classic cartoons - ironically this was the film that actually kickstarted the revival of interest in those shorts!
So getting the use of the characters was pretty cheap, especially because this was where Spielberg came in: the Disney ones were free, naturally, but his connections to Warner Bros and Universal made it easier to get Bugs, Daffy, Woody, etc, again because there was no real interest in doing anything with them!
The ones that didn’t appear (Tom & Jerry, Popeye, etc) were precisely because they were not owned by corporations that they had any connections to: King Features and and MGM did not want to play ball and asked too much to license their characters, but for some reason it was felt worth it for Droopy and Betty for their moments.
But it’s true that Bugs/Mickey and Daffy/Donald both had it written in that they had the exact frame count, lines of dialogue, etc, which was Warners' stipulation for being able to use them, also hence why Toontown is largely populated by Disney supporting characters, which would be kind of recognisable but not steal the limelight from the big "stars".
The film ends with Porky in tribute to the most well-known cartoon shorts ending, but when Eisner saw the storyboards he decreed that "no Disney film is going to end with Looney Tunes ending!" and so Tinkerbell was added - she actually closes the film with her fairy dust after Porky's line, for the best of both. Even though Pan wasn’t released until six years after the 1947 setting of Roger Rabbit, I like to think that these characters were always around in Toontown waiting to be discovered!
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