I think you are looking at things from an incorrect lens here as far as "the system" goes. To give some context, the music industry was a whole different animal when Bob Dylan started in the 1960s. The "establishment" back then could be represented by, say, musicians from the Grand Ole Opry type of tradition, and the long tail end of the crooner / sweet music / big band era. Maybe some of the doo-wop which got popular in the 1950s was kind of "establishment" by then.
Folk along with rock and roll were the rising youth movements of the time and I'm not sure the older generation at the time understood it very well. Today it does seem like much of top pop promoted music is half "written by committee" but I'm not sure that was the case back then (see Frank Zappa's take on this from the eighties, which I personally think is even more true today: https://www.youtube.com/watch?v=xP4wsURn3rw)
Look at the top of the charts from 1962 when Bob Dylan released his first album. (https://en.wikipedia.org/wiki/Billboard_Year-End_Hot_100_sin...) There's some R&B and rock for sure but also a heck of a lot of big band / jazz type instrumental (your Kenny Balls, Acker Bilks, David Rose, etc.), some country as well (Johnny Tillotson, Claude King, etc.), and cutesy pop numbers (the "Mashed Potato Time" is #3 for 1962).
The "folk music revival" Dylan started in was also fairly massive in the early 1960s but I would say at the time the top was represented by Peter Paul and Mary and the Kingston Trio (both are on the Hot 100 chart in 1962). Bob Dylan won't appear on the Hot 100 until 1965, #41 for "Like a Rolling Stone". (Of course, Peter Paul and Mary brought Dylan to a national audience with "Blowin' in the Wind".) In 1962 this wasn't even a decade out from when Pete Seeger / the Weavers got tangled in that McCarthyism drama, so it's fair to say that the whiff of anti-establishment the folk revival movement had was a somewhat justified feeling.
Of course, Bob Dylan went well beyond the folk revival. I personally don't get the vibe that Dylan was quite as anti-establishment or political as many of the others in the folk revival, nor do I imagine that he thinks of himself as a "rebel". He's more of a poet plain and simple; what makes him unique is more his words / lyrics than anything else.