The Punisher isn't the good guy, but the mobsters he takes out are also bad.
Like, these are still violent criminals we're following.
We're rooting for them, because we like them. They're still Bad People. ("Bad Man" slang meaning)
I root for Subaru et al, but I still say those books are about villains, from their perspective, as heroes of their own story. That they are just another branch of the Witch Cult, with a trail of atrocities behind them, grasping for power.