The strip is defunct now (but it used to run in papers) but My Cage featured several main female characters. But the focus character was male so the females were his girlfriend and co-workers.
Mostly men, admittedly. But I’ve also noticed it in books written by Agatha Christie and Leslie Ford despite their protagonists being strong-willed, contemporary, take charge women.
I’ve thought about this a lot and the problem seems to be that all the women live their lives in a restrictive bubble to modern eyes. They are wives, or mothers, or young aristocratic daughters. They don’t have jobs, which would interfere with their ability to play amateur detective. Neither do most of the other women, and the exceptions are actresses or writers or artists or, at most, nurses. All authority roles are filled by men. All danger is taken on by men. In a crisis, the women hang back and let the men handle it.
Nor do the women have the range of flaws that the men have. Women can be viragoes (a word I just read in Ford) or dull or unintelligent. They can even be the surprising murderer, surprising because nothing in their character hinted at that. The man are outsized in every direction and more interesting because of that. The reader would accept any man in a mystery as a murderer because they’re all written that way.
Think about Dagwood and Blondie. Dagwood is a supremely flawed character (in acceptable ways). He’s lazy, he shirks chores, he sneaks out to be with the guys, he’s a glutton, he’s totally dependent on his wife in a hundred ways. The strip is about his flaws every day. But until recently he was the sole breadwinner, which gave him license to loaf at home. Blondie now works, but somehow has hours every day to make him dinner (and never complains that she’s been cooking all day nor does her catering ever take place at a time to interfere). She is totally admirable, a slim beauty with amazing skills, unflawed - except occasionally she’s a stereotypical shopaholic. The strip retains its roots (after it jettisoned its weird beginning where Blondie is a gold-digging flapper and Dagwood is the scion of millionaires), the men-dominated culture that was American life until remarkably recently.
Ha! 
Exapno Mapcase: Library of America to the rescue!
In Phoebe and her Unicorn, Marigold Heavenly Nostrils is definitely female. There are emphatically boy unicorns and girl unicorns in the strip. Lord Divine Humility – whose schtick is hiding in the bushes because he’s just so darn humble – made a reappearance just last week.
Then we have a winner! OK, an exception. We can now say that not all main animal characters are male. Just 99.999% of them. But hey, progress!
From what Wikipedia says, this strip started life as a webcomic. But it’s in more than a single paper, so it can’t be disqualified that way.
There’s been some logical analysis, but I think we all know the real reason: all male comic artists are secretly gay furries.
So the hypothesis goes that lead anthropomorphized cartoon animals are often used for slapstick physical humor which does not seem to work with female main characters …
The natural follow up is if there are/have been any female acts that focus(ed) on slapstick physical humor or does The Stooges style fail if they are female? If the above is the reason then there should be pretty much close to none. Yet one does have to think more than 5 seconds to come up with Lucille Ball and I am sure there have been many others.
I am not so sure the hypothesis holds much water.
I think its probably similar reasons to why “he” is the default pronoun.
For better or (more probably) worse, male is the default for our society. If you make an anthropomorphic male cat, then the defining attribute of that character is that he is a cat. If you make a anthropomorphic female cat then the gender of the cat becomes as much of her defining attribute as her identity as a cat, which may distract from her nature as a cat. So if you just want to put generic cat in your comic you go with a male.
And, of course, he did at one point reveal that Rosebud the Basselope was…GASP…a female!
At the turn of this century, there was Wildwood, a strip by Dan Wright & Tom Spurgeon which featured two male leads and a female character nearly their equal. Spurgeon says while he liked the female character he didn’t get the hang of writing her dialog.
Yes, that’s very true. The sharks Sherman and Megan are a perfect example. When the strip needs a shark doing shark things, like stalking beach apes, invariably that shark is Sherman. Megan does stereotypical-human-female things like nagging her husband.
Says Freddy, anthropomorphic pig from a mostly-male anthropomorphic farm.
And how incompetent he is at work, rather than how much of a tyrant Dithers is. This has changed the tone a lot.
Does Charlottes Web count?
In any case, yeah I see it in video games as well. Bioware’s Mass Effect had aliens that were exclusively male. They even invented lore to excuse why the alien characters were (mostly) only male. Females of that race were rare and special.
I suspect it was a resources issue in that case, but one game artist commented in an interview ‘how would we make a female Turian anyway? Put breasts on the model?’.
Also, those familiar with the game will point out the Asari. A race of mono gendered blue space babes.
The more generic a cartoon character is, the more “everyman” he can be. Black cartoon characters are seen to represent black people, female characters are seen to represent females in general. But someone who represents all of humanity tends to look like Ziggy or Charlie Brown or a male anthropomorphic animal. It’s just the language of the comic strip.
The same reason most comedians are male: they can stand ridicule and indignity for our entertainment without giving us an uneasy feeling.
Ha! I suspected as much…
I remember that plot arc. In fact, it’s more or less why this thread. Before revealing that, he’d pointed out that all the animal characters in Bloom County were male. I got to thinking about that and realized that most of the comic strip animals I could think of were male and all the females were minor characters. This thread is partly to find out if things have changed in strips that my paper didn’t carry.