There are strong reasons to believe that this song pertains specifically to the film it was used in (Keeping the Faith), which tells a story of a Priest and Rabi falling for the same girl - hence the use of the yiddish word Pitseleh, which means "little one" - yet this song has a universal theme and feel: essentially regret over a relationship that was doomed, even if you were the one who destroyed it.
The song suggests emotional isolation from another person, because the protagonist is alone in the emotional depression that surrounds him and he believes that only he can truly understand it. He therefore wants to keep her from and so, in this respect, she is his "little one" (Pitseleh).
He starts with the self-reflective emotional relapse he is having:
"I'll tell you why I don't want to know where you areThen he starts into the stark explanations of their demise, darkly suggesting how he kept possible suicidal tendencies from her
I've got a joke I been dying to tell you"
"A silent kid is looking down the barrelAnd so continues his justification of their breakup, trying to advance a more benevolent rationale:
To make the noise that I kept so quiet
I kept it from you, Pitseleh"
"I'm not what's missing from your life now. I could never be the puzzle pieces"and that she should consider this one of life's tests
"They say that God makes problems just to see what you can stand"although, despite this, he concedes that he has succumbed to a choice more akin with his self-destructiveness - which is to end the relationship with her
"Before you do as the devil pleases and give up the thing you love"
Nevertheless, he utters his regret and sadness
"but no one deserves it"
He then goes on to describe the unavoidable sense of doom he brought to their relationship from the outset
"The first time I saw you I knew it would never last"by admitting the self-flagellating perception he has of himself
"I'm not half what I wish I was"as well as, more importantly, what he sees as his main flaw: rage
"I'm so angry, I don't think it'll ever pass"And yet, amid this emotional logic and certainty, he closes with a sense of frailty by being vague
"And I was bad news for you... just because"followed by a self-deprecating apology
"I never meant to hurt you"