Do you feel a need to wear pants while in public? Some people do, but not too many cartoon characters. Wolf Gnards analyzed the incidence of pants-wearing by cartoon characters and distilled the principles that animators tend to use when deciding whether or not characters should wear them. One of those apparent rules is that adult and male characters have more pants-free options:
Networks seem to demand more clothing on female and children characters, animals or not. For example, Yogi Bear's girlfriend, Cindy Bear, had to wear a skirt, while Yogi's crotch was free to the world. Or Gadget from the Chip & Dale had to wear more clothing than the others. No pants was obviously an option for the rest of the Rescue Rangers crew, but Gadget had to wear a jumpsuit, also known as, the maximum amount of clothing possible. Or take a look at the Shawn Bradley vehicle Space Jam and the introduction of Lola Bunny, a fully clothed female bunny. Making her one of the few clothed Looney Tunes characters. Likewise, The Tiny Toons were “tiny” versions of the adult Looney Tunes, and each character had their equal; Bugs Bunny to Buster Bunny, Daffy Duck to Plucky Duck, and so on and so on. Similar designs, similar personality traits, but clothed. The Tiny Toons mostly wore shirts or, at least, hats and shoes, whereas the adult Looney Tunes they were based on were nude.
Link | Image: Warner Bros.
THe bottom line is that characters were drawn as male first, and not having a need for clothing to determine their gender. The female versions had to be differentiated somehow from the males, and adding gender-specific clothing is the obvious option.
You'll notice that cartoon cows show a lot of udder, but nobody complains. If Daisy Duck were to sprout barenaked breasts, people would be up in arms.
According to TVTropes, a reason cartoon animals don't always wear pants is to show their tails and give a clue to what their species is.