Lyric discussion by alframsey 

Cover art for Lonesome Day lyrics by Bruce Springsteen

I think this song is about the initial reaction after 9/11, and a call for calm. Especially when he says "Hell's brewin', dark sun's on the rise This storm'll blow through by and by House is on fire, viper's in the grass" and "Better ask questions before you shoot Deceit and betrayal's bitter fruit It's hard to swallow, come time to pay That taste on your tongue don't easily slip away"

To me it all seems like he is telling everyone there was a need to consider what we had been doing wrong to cause something like this (not that it can ever be justified), and not to follow knee jerck reactions.