Young wrote this in response to Lynyrd Skynyrd's "Sweet Home Alabama," in which Young is told, "Southern man don't need him around anyhow." "Walk On" wasn't so much directed at the guys from Skynyrd (their feud was more good-natured than most people realize), but more towards the few southerners who felt some animosity towards Young for calling them on their inability to comply with the changing standards during the civil rights era.
This song functions as a wistful ode to how life never stops changing, so you might as well accept it and walk on (rather than dwell on small things like the hostile southerners). It's characteristic of the melancholy and pessimism that permeated Neil's work around that time, particularly On the Beach.