As you guessed, cookie-cutter means the same thing -- structure, flavour, etc. It comes from the idea that a cookie cutter (the metal die used to shape cookies) makes the same thing every time, and there is no artistic appeal to something that anyone could just 'stamp out'.
I hear this a lot with essays. The traditional five paragraph essay structure is considered cookie-cutter, since you just fill in facts and information.
Typically you will see this phrase used with creation -- architecture, painting, music, film, television, writing, speech, etc.
As for it being pejorative, yes, it is insulting to tell someone that their work is cookie-cutter, since you effectively tell them they did something anyone else could do.
The example you have means that if you go at music only for the money, you will fail, because emotion, the part that the cookie cutter leaves out, is what truly fuels art.