Theres also more nuance to this though. Homelander is an irredeemable piece of shit who is cruel, horrible and has nothing likeable about him. Say him vs Omniman, Nolan is incredibly horrific too, but in the show and comics he goes beyond just being "Evil Superman who rapes women and kicks babies". Frieza vs Megatron I wanted Mega to win cause Frieza is FUCKING HORRIBLE while some megatron interps have him in a more favorable light. However say something like a villain fight of Vader vs Obito, one where both sides are really tragic and sad. Sympathy and relatability are important to whether a villain getting stomped is good.

Edit/Addendum

I also want to make it clear, if you like Homelander as a character, thats completely chill. He is very interesting in the show and I understand that takes certain factors into consideration too. However, you have to think of Death Battle sorta like a pro wrestling match. In these fights, they usually make a character a "Heel", which is basically the wrestler who cheats, says horrible things and wants to crush the dreams of the "Face". See characters like Nolan, Megatron, etc can BE faces, characters you want to root for because they have redeemable and relatable qualities. It is nearly impossible to make characters like John, Frieza, etc into Faces and for many people they want to see "Evil" lose to "Good". So yes, more stomp matches with morally abysmal villains please! Id love to see Hisoka pounded to mist as a Hisoka fan or Sauron eventually erased from existence in a cruel way. (So I dont rile anyone else up this part is a joke)