"Not worth the paper it's printed on" - wrong meaning?

Solution 1:

“Not” in comparative forms typically means “less than”. For instance,

I’m not as tall as Michael Jordan.

means “I am less tall than MJ”, rather than “I am not exactly the same height as MJ”.

So in this case, “it’s not worth the paper it’s printed on” (and parallel constructions like “it’s not worth waiting ten minutes for”), not means it’s worth even less than the paper is — and that’s already a negligible amount. So it means something is worth a really really negligible amount — or even, as @Martha suggests, worth less than nothing.

Solution 2:

This usage of "not" includes an implied "even": it's not even worth as much as the paper it's printed on, i.e. it's worth less than nothing.