I read an interview where frank said that his intention was for Dune to be a cautionary tale about the dangers of charismatic leaders (which is to say, the "classic" hero archetype). Which - for the first book - tracks pretty well. The free are basically just used as cannon fodder for Paul to win back his power (and a lot more), then when he wins, he sets them loose on the universe because he can't control them.
The trouble I have with that though is that he goes on to contradict that point in later books, but I won't get into that because I don't want to spoil anything for you