If the problem is that not many people read SF, how can popular SF books be part of the problem? Are you supposing that if not for popular books like Dune, people would read a wider variety of other SF works? I don't think that's how it works.

I think popular SF books are important for bringing the genre to a wider audience. Someone who is not familiar with the genre might pick up Dune because of the films, and sure, maybe that's all they'll read, but maybe they'll enjoy it and pick up some more.