Time is money, and the materials and tools are not cheap. Even at $3000, a luthier made bass guitar is not bad once you think of all of the aspects.
How much it's truly worth is up to you. If you don't think a persons skills and time are worth that much money, that is between you and yourself.
Just because bass X at $1000 looks like bass Y at $3000, doesn't mean there is anything the same about them, besides the shape.
It doesn't mean they're that different either.
In manufacturing people can take advantage of economies of scale to simultaneously improve quality while reducing cost.