Dune is a masterpiece.
The reason so many people don't get it, and I admit to being one of those after my first reading, is that most people only read it once, or don't finish it because they are waiting for the story to be told to them and not invest any part of themselves in it.
My suggestion is to read it again, but this time keep in mind Jesus Christ and the politics of the day. Then, read it again but this time remind yourself of the political and social upheaval that was occurring in the world when it was written. Then, read it again, but this time keep in mind the idea of population explosions, ecology and finite resources. Problems that afflict us today. Then read it again, but with an eye on what it really means to be free. Then read it again.
No human art is timeless. Dune is trying though.