Sonic Youth are less marginal, at this point, because they have a larger audience and a more accessible format. And I think one of the things it has to do with is a conscious, deliberate relationship to the marketplace. Which, in the case of Sonic Youth, has been extremely good for their music. I can’t think of any band of the past five years that’s "sold out" to better effect than Sonic Youth. They’re more interested in writing tunes, they’re readier to work with relatively tight and traditional constructions, song structures. And it so happens--much to my surprise, because I always thought they were an interesting band with a good sound who were incredibly overrated by their cult--they really turned out to be good at this.
An interesting thought that runs counter to the conventional wisdom. Selling out is usually regarded as an act of creative defeat, accepting limitations on what you can do in exchange for greater financial security. The fuzzy relationship between art and commerce has always been under-specified in indie music narratives: a band should be successful enough for its members to quit their day jobs, but not quite so successful as to be rich, whatever that might mean. One has to be in the nebulously defined middle space. This serves valuable (and exploitable) functions. Bands that don't make a lot of money function as excellent points of entry to the scene as a whole--their shows are cheap, their albums are cheap, and can therefore be purchased by people without much disposable income (ie teenagers). Minor and regional labels like this system because it leaves vague what success should look like--no one on the indie scene wanted to get rich and therefore lose their credibility, and who's going to hire a lawyer to negotiate a contract? The system as a whole requires all its limited financial resources to be continuously circulated to keep the system afloat--disposable income must go to the right stores, labels, clubs, etc. Developing a stigma against those who allow their money to leave the system becomes crucial to keeping it at work, but the stigma can't be about money--who cares about money?--and so becomes a narrative of artistic decline. Leave this comfortable and experimental world and your work will suffer.
A number of musicians have had this problem, though no one much considers the possibility that decline is frequent in long-term careers, and not everyone has a long-term career in them. Because major label contracts come (/came) later in a career, bands were more likely to have hit the limit of their creativity.
Except, as the case of Sonic Youth demonstrates, that's not true. Some people respond to more responsibility by becoming more responsible. Sonic Youth's attitude became one in which it tried to maximize its talents by seeing how much of their interest could fit into a form acceptable to a broader public--in this respect, they were quite successful, and are still resented for taking the money and becoming much, much better than they were in their indie days.