It's become so common that we don't even notice that it is a philosophical rumination rather than a direct imperative. It's a bit of a social dilemma. On the one hand, you do want the salt. On the other hand, you don't want to boss people around lightly.
So you split the difference by saying something that literally makes no sense while also conveying the message that you're not treating them like some kind of flunky.
Cognitive scientist Steven Pinker explicating the phrase: “If you think you could pass the salt, that would be great,” as cited in Of Thought and Metaphor in yesterday’s Toronto Star.
“We have to do two things with language. We've got to convey a message and we've got to negotiate what kind of social relationship we have with someone,” says Pinker.