Popular culture is popular.
These are absolutely science fiction (or fantasy or whatever label you want to apply), but they are popular culture movies, which are considered must-watch films for anyone, not just a science fiction (or fantasy) fan. The majority of people watching these films (or who watched them many years ago when they were new) would not be considering them in terms of science-fiction.
The number of people that have seen these two films (even the intersection) is phenomenally large - I'm sure considerably larger than the number of people that watch/read the majority of other work that the site focuses on.
This is why Harry Potter gets so many views - the series may be the only fantasy books that many of its readers have read or will read. Likewise Doctor Who (this may be less true in the US than in Commonwealth counties?) - the series may be the only science fiction show that many of its viewers watch/have watched/will watch.
(I think the element of mystery in Harry Potter and Doctor Who help here too, since that naturally lends itself to questions. If Harry Potter hadn't been finished by the time the site started, I imagine we would have vastly more questions about it. Likewise if Lost was still airing when we started, that would (a popular culture TV show mystery) be a significant source of views).
This material isn't seen as "science fiction" or "fantasy", it's seen as "films" ("TV", "books"). That means that the potential audience is vastly larger.
IMO this also calls for an element of caution. Although these questions pull in large views, the value of our site is in the deep specialist knowledge about all science fiction and fantasy, not just the mainstream stuff. If the people viewing these questions end up taking a look at other questions on the site, or asking their own (good) questions, or answering other ones, then that's great. If they are just looking at that single question, then that's great for the metrics, but is it really adding value to the site?
IOW, I think it's great that we have these very popular questions, and I hope we continue to have them. However, I don't think we should do anything to go out of our way to have more questions about mainstream content than on lesser-known sci-fi/fantasy.