I'm going to be so honest
In my opinion there are many factors to take in account.
I've noticed that there are different types of franklydear shippers and applebite shippers in the fandom, especially around the early days of the fandom
The franklydear and applebite shippers that are genuinely chill and are pretty cool.
And the ones that are God damn unbearable to be around. (You mostly find them on TIKTOK)
Those categories of franklydear shippers are usually the ones that hate any ship that "gets in the way" or "rips" their otp apart. They'll basically harass or badmouth frank or Eddie yumme shippers (especially women yumme shippers) oc x Frank or oc x Eddie shippers (especially if their women OCs. They do that under the guise of "Frank and Eddie are gay! Shipping them with a woman erases their queerness" when in reality, they just don't want anyone shipping them apart. They also harass flowerfly shippers which is literally shitty to do. They also get super defensive when you say that franklydear is technically not cannon because it's not confirmed to be the endgame ship on the website yet. But like my point is, it's usually those types of franklydear shippers who don't fw applebite and I honestly don't know exactly why other than my guess being that if they're closed minded to that then they are definitely closed minded when it comes to applebite.
Because for applebite case, if you were in the early days of the fandom, there were QUITE A FEW applebite shippers that were toxic and problematic had art that made people think poorly on the ship.
Like some made barnaby abusive or Wally abusive. Or they were following with the idea of Wally being evil. But those types of applebite shippers always mischaracterized both of them and onlookers saw that and just had a bad impression of applebite.
(There was this one applebite shipper who made this Applebite au, Hypnotic au, and it did a lot of damage to applebite's reputation. Even though it was a vent au and I don't think the creator of that au ships applebite or is even in the fandom anymore.)
But also it stems from the fact that some people infantilize Wally and believe that he's too mentally disabled to understand love, sex, and anything adult related and view barnaby as his parental figure. (I fucking hate those types of people ngl) Even though Wally is a full grown adult.
Also the "can't ship applebite cuz barnaby is a dog" believers are full of shit and actually don't believe that, they just want an excuse to not ship applebite or trash people who do.
Not all franklydear and applebite shippers are like that, it's just a handful of em. If you don't ship applebite just because it's not your cup of tea that's perfectly fine or if you only really ship franklydear but no one else really but don't harass people for not shipping them, then literally you're Giga Chad in my book. This was just a post of what I think is the reason why some (KEY WORD: "SOME") franklydear shippers trash on applebite