They're the protagonists of both shows because both shows are comedies where the object of the game is to squeeze as many laughs as possible into a half-hour of programming. And so the father figure is a figure of mockery who provides the greatest outlet for those laughs and the kind of buffoonish humour that both shows are trying to portray. If the wives were the protagonists and greater relied upon as figures of mockery, and the husbands instead occupied the role of the put upon straight man who sighs and rolls his eyes at the ridiculous antics of his silly wife, then audiences of today would also probably use that as an excuse to call the shows misogynistic, no?

Damned if you do, damned if you don't. If I too myself too seriously and didn't enjoy the antics of Homer Simpson so much, I'd argue that it's actually misandrist, if anything.