I've been thinking about your Powderfinger thread (http://metachat.org/index.php/2005/10/18/powderfinger_by_neil_young) and I looked up this page again (http://www.thrasherswheat.org/fot/powderfinger.html). That guy Mark brings up a number of really good points, but he misses some.
Any particular story aside, it looks like (sounds like?) it's about a young man, alone, and having to make his own decisions ("you'd better call John" = "I don't think I can handle this alone"). The whole second verse is just about that. It's also about the legacy that you're led into. This guy's still living at home, hasn't struck out on his own. So he's something of a victim of his family's way of life/location/etc. He's got some bad wisdom been passed down to him by his family; they've told him to stand and fight, but he's a thinker (and a lover) not a fighter. "Never stopped to wonder why" is the force of tradition telling him what to do (and his father's words). Who knows? In a different life, this kid could've been at college when this happened.
I think a big part of this is the influence of the older generation on the individual. Whether law and order or parents, this kid's (I say kid, myself just 25!) a victim of external forces. What sticks out at me is that they shoot first. It seems like some kind of government vessel (the "deliver the mail" line suggests that it looks like an official boat). So he's sandwiched between corrupt law enforcement (they shot first! that still gets me. Bastards) and his family's way of life, when he should be worrying about the things a normal red-blooded 20-something is worried about (hence the line "remember me to my love"). A war-like society creates a vacuum as the older men die and the younger are forced to take their place prematurely. He never even had a chance, as the guy on that website said.
He also said "If anything, 22 is a *victim* of Powderfinger". Powder on the finger comes from firing a gun, of course. He's living somewhere where things are ruled by gunfire rather than the kind of thinking he's used to doing. Like I said, in another world, he might've had a chance. He's the kind to solve his problems with thought and discussion living in a world where violence rules the day. He was right, I think, where in 3.9 he says "protect me from "protect from a society where accounts have to be settled with guns, where lawlessness parades as the law; protect me from my fate; protect me from dying." But then he doesn't get the line "Cover me with the thought that pulled the trigger". This seems obvious to me (as a libertarian/anarchist); it's about paternalism (both in government and homelife, as I said above). The government that shot him did it "for his own good" (like in Cool Hand Luke; "Wish you'd stop being so good to me, Cap'n."). "Cover me" suggests that this "benevolent" thought behind this brutal action is supposed to comfort him like a blanket. Which is, of course, sarcastic coming from Neil (though 22 probably meant it; part of the reason why it took him so long to shoot is he was conflicted out of loyalty for family and gov't, the both of which ended up being the death of him when they clashed); the kid's dead so fat lot of good it did him.
It seems like an individualist dirge over the rise of governmental control and "traditional values". I know that "the powers that be" can be religious, but I've always thought of it in a political context (http://en.wikipedia.org/wiki/The_powers_that_be). If you add the religious element, then you've got a triple threat of "authority." Neil's lesson is that we ought not to put too much stock in the law or tradition (and possibly religion) and learn to think for ourselves or we'll end up "wonderin' what to do" when the first shot hits the docks where we live. "It's less than a mile away." I'll refrain from using the phrase "cautionary tale" because I already sound enough like That Pretentious Music Jerk. But I've listened to the song a bunch of times since you uploaded it and these few thoughts have been banging around inside my head. I thought I'd share, even if it's been awhile since you asked.
Thanks, man. I love a good mystery.
Yours in rock,