If there is a machine and unlimited energy to run it (we'll accept this for the purpose of this argument) capable of assembling protons, neutrons, and electrons
into various items, someone will still need to write the programs that will determine the sequence in which these building blocks will be put together.
Some things, like raw alcohol, are probably simple enough for the lay-person to just punch the requisite molecule into the machine and push the "replicate" button,
but anything more complicated, including something as seemingly simple as Coca-Cola is going to require thousands of separate molecules in precise ratios
to come close to The Real Thing.
If goods become meaningless, it's these recipes that will be what hold the real value. If it's just as easy to build a Harrier as it is a bicycle, the people who designed
the Harrier and the guys who figured out how much molybdenum you need to make one are going to be fiercely protective of that information. Presumably they'll
make it available to you, at a significant price.
Just what form currency would take in a world like this remains to be seen. Gold is obviously worthless as is anything physical. Who knows.
As for the notion that we'll simply pirate the plans for the stuff that we want, I imagine that the design firms would have locks on their designs that make current
copyright protection look like, well, current copyright protection.
And before anyone says that they'll simply reverse engineer the things they want, as a test I want you to go out to the most expensive French restaurant in your
city, order the bouillabaisse, then go home and replicate it exactly. Chances are you won't be able to do it. Translated into our example this is akin to trying to
build your own Scarlett Johansson-bot, and you get the face right, but she has the lower half of a goat and talks like James Earl Jones.