What exactly is the difference between knowing how to "set up" a machine and "programming" a machine. I know quite obviously that programming would be writing the program rather it be done by hand or with cad/cam software. I've been looking at jobs and a lot will say must be able to set up the machine, programming would be a plus. Would setting up mean just getting the machine ready for a job? Please go into detail as I need to learn as much as I can.

Im not very good at explaining some things so Ill try my best lol.

Setting up a machine, from my experience, consists of changing out tooling, setting offsets, touching off tooling, setting all the parameters needed, etc. You would get everything in order for that machine to do a production run so that the operator would push the 'go' button and check the parts.

Programming consists of choosing the proper tooling to use (taking in account the longevity of inserts/tooling, type, material, etc.), drawing the part (if using CAD/CAM software) or writing the code. Taking care of all the details so that you can hand a program and a print to a set-up man and he has everything he needs to do the above stated.

I hope that I explained it well enough lol.

Real Simple! You have to be able to set up a Machine for a Parts Run, just as the adds say!
Experienced Machinists will know what the Material should look like, where on the Table to place it, what tools to use, what clamping is required and such.