Dylan wrote basically one album worth of explicit “finger pointin’ songs”. After that he branched out into other things and being far more of a rock singer/songwriter rather than a folk singer.
His protest songs came very early in his career which is as much a product of his idolization of Woody Guthrie as any deeply held beliefs.
He has never gone to protests and joined in all the liberal causes. He was always more into music than political beliefs. His contemporaries from the time, who were into the protests and movements, said Dylan was (and presumably is) apolitical.
Is the song most likely about disaffected youth? Yes. Is it hiding some revolutionary call in its lyrics? Highly doubtful.
"Johnny's in the basement
Mixing up the medicine
I'm on the pavement
Thinking about the government"
"Maggie comes fleet foot
Face full of black soot
Talkin' that the heat put
Plants in the bed but
The phone's tapped anyway
Maggie says that many say
They must bust in early May
Orders from the D. A.
Look out kid
Don't matter what you did
Walk on your tip toes
Don't try 'No Doz'
Better stay away from those
That carry around a fire hose
Keep a clean nose
Watch the plain clothes
You don't need a weather man
To know which way the wind blows"
http://www.bobdylan.com/songs/subterranean.html