You focus too much on the "speech" part, it isn't like zero cost software is compared to beer. The "free as in speech" is used to disambiguate between the "price vs freedom" use of "free", not to put any connotation between software and speech.

"Free as in speech, not beer" is really a short way to say "when we use the word 'free' here, we do it with the meaning that is used in the phrase 'free speech' as opposed to the meaning used in the phrase 'free beer'".