From the three I read (stopped with children of dune) the main theme is that blind loyalty is bad, but there is some stuff I would classify as reactionary:
there is an offhanded comment that feudalism is the most efficient way to govern a planet, this point is never brought up again to be argued against even though the system entrenches the blood feud that causes the first book to happen Edit: I cannot find this comment anymore, I may be crazy, should be within book 1 of Dune
Dune is a white savior inside a white savior: Paul's portion of this is forgivable as Messiah and Children of both reference the idea that he was the wrong choice, but Liet-Kynes is also an off-worlder. Any fremen who has traveled to other planets (even if it's a rare occurrence, what about smugglers or those taken for the Harkonens slave pits) could have had the knowledge of other planets required to tell the dream, but it had to be an outsider who organized and lead them.
Herbert's obsession with how tough environments create tough men; to me it read like the cycles of history hogwash. After all these tough environments weren't enough to save the historical people the fremen are based on from colonization
