What I take to be the core notion of "selling out" is the idea of deliberately altering your musical style for commercial purposes -- producing the song differently from how you would have at the label's request, making the songs shorter to be radio-friendly, that kind of thing.
I think it's clear enough why selling out in this sense gets a bad name. It's possible, of course, that music produced in this way will be good. It is, however, quite easy to see why one might anticipate bad results. In particular, it seems very likely that this method will wind up disappointing your core audience. Thus, even without adopting an unduly moralistic view of music or an ideological opposition to "selling out" you could still be disappointed to see a band you like appearing to sell out in this sense.
Now, the perniciousness of that notion of selling out leads to a kind of second-order worry. In principle you could ditch your indie label in favor of a major label and still keep your sound pure. In practice, however, maybe you worry that having signed a contract you'll find it difficult to resist pressure and stay true to your vision. It's easy to say you'll never give in, but we all know that things look different once you've gone a little ways down the road. 1Ls at elite law schools are famous for saying they're not going to go work for big corporate firms, and about-to-graduate 3Ls are famous for going to work for the firms they said they would never work for.
Thus, a practical worry develops about a band that "sells out" by signing with the big label. Going to a major isn't bad per se but it's perhaps indicative that bad things are likely to happen. Concern strikes me as at least somewhat warranted.
The trouble, in my view, is when this shifts from being a practical worry to an ideological one. Logically speaking, I see no practical reason whatsoever to think that bands selling their music to major corporate advertisers will have a deleterious impact on their work. The opposition must be a purely ideological one -- it's against the spirit of the music to partner with major corporations. And the trouble here is that anti-selling out ideology, at the end of the day, makes very little sense. It's a fundamentally Jesuitical enterprise based on goofy, arbitrary decisions.
What good does it do you to eschew Honda's money when they want to make an ad when, presumably, your band is going to go on tour and that tour is going to involve riding in vehicles made by major auto companies? It's not possible to participate meaningfully in modern society without being deeply implicated in the web of corporations that tie us all together. I use electricity and so does Ian MacKaye and together, he and I and all of you are partnering with the energy companies to destroy the planet. The only thing to be done about it is to try to support political candidates and movements likely to produce better public policy.
One can (and, indeed, probably should) boycott specific companies who have practices you abhor, which creates incentives for firms to try to avoid abhorrent behavior, but the idea that one could somehow opt-out of the entire system by not letting one's music be used in TV ads or not signing with a certain record label is silly. It's telling that Kurt Cobain had intense thoughts on the nature and significance of not selling out and was also a horribly depressed heroin addict who wound up killing himself; getting too obsessed with this stuff isn't something healthy people should be doing.
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