I think that's more of JY screwing up than people not understanding -- Xiao Feng is simply just a much more engaging and interesting character. I get that Duan Yu is the one tying together most of the major plots, but it's XF who actually resonates with readers because he lives the unfortunate wuxia hero life while Duan Yu is just watching from the sidelines most of the time.
Even if it's inaccurate, treating XF as the main character is absolutely the right move in adaptions and given a choice I'd rather him be the main character in the novel as well.