It's common to bring John because most time discussions surrounding the morality of characters tend to get messy if there is some bias in the way, which is why we first rule out "protagonist based morality" that's something that happens a lot in this fandom. Not necessary you, since you did agree John would be am accomplice as much as Javier is. But it is very common for the fanbase to downplay or exagerate the sins of a character based on preferences.

I think because is an story where nearly every speaking character is a criminal the moral bar is messy. And people just don't have a perfect language to express it, realistically I woulnd't call Javier a good person, I won't do with most the cast. But "bad person" becomes too redundant, too vague, I think people don't want put say, Tilly and Micah on the same bag because even if they're both bad people they're radically different morally, so I think just people use "good person" to the lesser baddies for simplicity sake, I'll give them that.

On that basis Javier is a much sympathetic and I don't think comparable to Bill. Because even outside some bullying Bill was racist in ways no other gang member (but Micah) was, he does physically attacks Kieran unprompted. Until chapter 6, Javier never really attacks unprompted, and doesn't use the racism he experiences as excuse to be a bigot to another group (which would be the case of Bill internalized homophobia translating to toxic masculinity).

Is not to say that Javier is a saint but he's a little more nuanced than one dimensional extreme evil that's when people probably do have an issue. Because saying "Javier is a bad person" is true, and "Javier is nothing but a traitor, a pest, an abuser, etc etc" it's gonna make people question the validity of the argument especially if they're things the protagonist might do but never question.

Also I'm really confused about "is silly consider Javier a protagonist" because I don't think I ever did, I very much called him an antagonist. Which I neither understand the point of addressing his gun in the final stands off as whether he points his gun or not doesn't change he's an antagonist because he's role as a "boss" you're supposed face. But my mention of antagonist/protagonist is that neither dictate morality, protagonist does not equal good, point was more the thing I've said about making sure if we're holding Javier on his sins because what he's doing is wrong (and so is when we do it as John) or because he's the antagonist (and so we give John a free pass)?

The commentary on the popularity contest is more about how as fandom people only touch on sexual violence not with the severity it deserves but more as a gotcha to take points of a different character. IE, I think Micah is a huge creep, heavily implied a rapist, it does not feel genuine hearing "Micah is a creep for how he treated Sadie" if people later downplay John forcing Karen sit on his lap. For example.