Dylan's intended meaning (if indeed there is an intended linear meaning) is hard to see in this one, but there are some clues. We also can make assumptions based on the context of the Rough And Rowdy Ways
album, which is heavy on Biblical imagery and Christian ideas, as heard in "False Prophet
," "Goodbye Jimmy Reed
," and "Murder Most Foul
One verse, in particular, gets the Christian viewpoint across: I feel the Holy Spirit inside
See the light that freedom gives
I believe it's in the reach of
Every man who lives
Keep as far away as possible
It's darkest 'fore the dawn (Oh Lord)
I turned the key, I broke it off
And I crossed the Rubicon
The "holy spirit" is frequently referenced in Christianity. It's basically the "spirit of God" and can inhabit the faithful or convert the unfaithful. It's what empowers Baptists to handle deadly snakes and evangelicals to sing their praises.
Freedom ("see the light that freedom gives") is also a concept Dylan has discussed in relation to "finding Jesus." It may seem strange to non-Christians (who tend to view the faith as an authoritarian one), but for many, Jesus promises freedom. It's not freedom in a political sense, but freedom from sin, which can be viewed in all sorts of ways (from freedom from "the fire and brimstone of Hell" to the same internal "freedom from self" sought by many Eastern religions).
It's tempting to say Dylan is referring to his own Christian conversion experience, but we really don't have any evidence for that beyond the fact that he did convert (some time back in the '70s) and that his song seems to be discussing "crossing the Rubicon" into Christian faith.
For a taste of Dylan's most overtly Christian music, check out songs like "Pressing On
" and "Gotta Serve Somebody."