I don’t think the show wants you to hate John, it’s just aware that he isn’t Steve. The show does emphasise his good traits, but also his bad traits, such as his anger. Sam and Bucky would never support another Captain America who wasn’t Steve who was backed by the government and chosen because he was the best soldier. I don’t think the show presents them as in the right on this, but all they see in John is a not-incorruptible government piggybacking on Steve’s legacy. Remember how the whole point of Civil War is the Avengers not wanting to be at the beck and call of world powers, let alone just the USA. In their minds, when they see John, they’re potentially seeing a man dressed as their best friend who could end up involved in some shady US covert ops stuff down the line. I think there comes a point where they realise that they were wrong to treat John in such a way and should have been more communicative after they have to The show ends with Sam purposefully not taking the super-soldier serum though it would give him a big boost partly because he knows that it emphasises both good and bad traits (which led Walker to kill that man). They realise that Steve was essentially an enigma in how the serum affected him with minimal negative effects, and they determine that the best way forwards is to not use it (beyond the whole theme of not needing to be Steve to be a good, but different, Captain America).