The book is about power and the limitations of power. An over riding theme in all of the books is that you have these incredible powerful people but they are for the most part helpless victims of circumstance and their own arrogance. Look at Paul and Leto II. Both were unimaginable powerful men who were trapped by their power.

Movements and ideas on the other hand are incredible powerful in Herbert’s books but they are destructive and uncontrollable. It is true that conflict between the groups is not well developed but that isn’t because the main conflict is with the planet it is because the main conflicts are internal conflicts and conflicts inside the Atreides household.

Finally a book isn’t flawed because it reflects the attitudes and beliefs of the times or the person who wrote it instead it is what makes them worth reading. You don’t have to agree with those ideas but seeing them isn’t a flaw.