I don't quite get this sentence:
What is the son but an extension of the father?
(from Dune by Frank Herbert)
Does it mean "Can the son be anything else but an extension of the father?"
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You do get it, that is exactly what it means. The only difference between "What is the son but an extension of the father?" and "The son is an extension of the father" is that the former phrases the statement as a challenge to the listener to present an argument countering the statement whereas the latter is a simple statement of the speaker's opinion.
The former is, however, a rhetorical device, the speaker does not really expect to be challenged.
It should also be noted that you as the reader do not need to agree with the opinion expressed, and neither does Frank Herbert. The only person who is forced to accept it is the character.
Your interpretation is more or less correct. With that type of construction ("What is A but B?"), the author is expressing the following idea: "People might not usually think of the son in the way I am going to describe, but I am proposing that the son is, in fact, just an extension of the father."
"What is A but B?" suggests that this comparison between A and B might not be obvious to everyone, but that if you think about it, A is really the same thing as B (or B is another way of describing or thinking about A).
For example: "What is life but a prolonged march toward death?" In other words: "People might not typically think about 'life' in the way I'm about to describe, but if you really think about it, you will realize that life is nothing more than a prolonged march toward death."