Nobody (afaik) is saying that jQuery chosen isn't better than a bunch of checkboxes.
The point is that <select multiple> (without javascript enhancement) is horrible and (imho) unacceptable. And no, it is not because we found situations in which it is not a good idea. It is because it is never a good idea, never.
The solution I'd propose (and Daniel also mentioned this various times here and elsewhere) to output checkboxes as fallback and an interface like "jQuery Chosen" as enhancement.
-- Krinkle