From the wiki:

"Maggie's Farm" is frequently interpreted as Dylan's declaration of independence from the protest folk movement. Punning on Silas and Laura McGhee's Farm, where he had performed "Only a Pawn in Their Game" at a civil rights protest in 1963 (featured in the film Dont Look Back), McGhee or Magee's Farm recasts Dylan as the pawn and the folk music scene as the oppressor. The middle stanzas ridicule various types in the folk scene, the promoter who tries to control your art (fining you when you slam the door), the paranoid militant (whose window is bricked over), and the condescending activist who is more uptight than she claims ("She's 68 but she says she's 54"). The first and last stanzas detail how Dylan feels strait-jacketed by the expectations of the folk scene ("It's a shame the way she makes me scrub the floor" and "they say sing while you slave"), needing room to express his "head full of ideas," and complains that, even though he tries his best to be just like he is, "everybody wants you to be just like them".

The song, essentially a protest song against protest folk, represents Dylan's transition from a folk singer who sought authenticity in traditional song-forms and activist politics to an innovative stylist whose self-exploration made him a cultural muse for a generation. (See "Like a Rolling Stone" and influence on The Beatles, etc.)

On the other hand, this biographical context provides only one of many lenses through which to interpret the text. While some may see "Maggie's Farm" as a repudiation of the protest-song tradition associated with folk music, it can also (ironically) be seen as itself a deeply political protest song. We are told, for example, that the "National Guard" stands around the farm door, and that Maggie's mother talks of "Man and God and Law." The "farm" that Dylan sings of can in this case easily represent racism, state oppression and capitalist exploitation.

In fact this theme of capitalist exploitation came to be seen by some as the major theme of the song. In this interpretation, Maggie's Farm is the military industrial complex, and Dylan is singing for the youth of his time, urging them to reject society.