In my own experience, the “stuff everyone seems to misunderstand” about Alice’s Adventures In Wonderland is that it’s supposed to be funny. I’ve seen many people fail to “get” the Alice books because they come to them expecting a fantasy adventure story or a conventional fairy tale. Whereas IMHO the closest parallel I can think of is the Monty Python movies, where the overall storyline is mostly an excuse to string together a series of comedic scenes. (Although a recently revived thread about Monty Python and the Holy Grail makes me wonder how many people understand what those are, either.