I dunno. That's more of a villain vs. antagonist role. A villain is always evil, but an antagonist can be either, depending on who the protagonist is. I don't so much see Wile E. as a villain, and frankly, I'm far more sympathetic to him than the Road Runner who's either completely obvious or sneakily sadistic depending on the cartoon. Elmer's not a bad guy, but he's an antagonist to Bugs being a hunter and all. Sylvester, same deal but he's a little more devious. Yosemite Sam is no doubt a villain.
Two cartoons tend to portray a less-antagonistic Yosemite Sam:
From Hare to Heir features Bugs Bunny as the one who grants 1 million pounds to Sam (Duke of Yosemite) with the condition that every time Sam loses his temper, a fine will be deducted from the 1 million (300 pounds, which is subsequently increased to 400 pounds per outburst). During his extended stay, Bugs's presence tends to frustrate Sam with each passing moment, and by the time Sam finally gets his temper under control, Bugs remarks "I haven't got the heart to tell him he's used up all the money" as the cartoon ends.
In "Honey's Money", Sam marries a wealthy widow, only to be turned into a henpecked husband who now has to spend quality time with he son Wentworth, which involves giving horseback rides to Wentworth, tossing a ball into the street (which Sam has to retrieve himself), and putting alligators into a swimming pool, only to have them land on Sam after they get splashed out of the pool, among other things. Even though he considers leaving home, he ultimately relents and goes back home, thinking that all the money actually is worth all that trouble.
We also see different aspects of Daffy: the zany screwball of the 1940's and early 1950's, as contrasted to the later years, when his darker side was featured more often as the years went by, especially when playing second fiddle to Bugs Bunny, or as Speedy Gonzales's secondary foe from 1965-68.
Still other cartoons tend to portray him as a thorn in the side of other characters, such as Porky Pig (
Yankee Doodle Daffy, My Favorite Duck, The Ducksters, The Prize Pest, Thumb Fun, Fool Coverage, Dime to Retire, et al.) and Elmer Fudd (
To Duck or Not to Duck, A Pest in the House, Rabbit Fire, Rabbit Seasoning, Duck! Rabbit, Duck!, Don't Axe Me, et al.), and then there are a handful of cartoons in which Daffy is a henpecked husband with marital problems such as
His Bitter Half, which is similar to
Honey's Money with a few major differences: Daffy's Wentworth is an impish, mischievous brat (in comparison to Sam's Wentworth, who is more innocent and naive), trouble at the carnival shooting gallery, and at the end, Daffy packs up and leaves without his feathers and money.
Other "henpecked Daffy" features include
Quackodile Tears, where Daffy's wife makes him sit on the eggs in spite of a mix-up involving a misplaced alligator egg, and
The Henpecked Duck, which involves Daffy practicing a magic trick with a disappearing egg that doesn't reappear until the end when Daffy asks Judge Porky for one last chance.