This song is about the dark side of country life. Bobbie calls it unintentional cruelty. The movie based on the song tells that story in a lot more detail.
A young man in a small town commits suicide, and hardly anyone cares. But by the end of the song (and movie) you realize that’s partly because death is so frequent where these people live. People who live in physically dangerous situations depends on a strong sense of purpose and morals to keep moving forward. Another reason hardly anyone cared about Billie Joe killing himself is because they never thought he was cut out for life where they lived. So they aren’t surprised that he died.
The movie tells the story from Billie Joe’s point of view too. He was a smart guy with a lot of imagination who wanted more in life than a small town had to offer. Small towns are too small to support most of the careers that depend on Bachelor’s degrees, which means that most people who get Bachelor’s degrees move away and never come back. That’s called brain drain.
That leaves teenagers who want more than a small town can give them with very few role models for how to get there. It also means that most people who get Bachelor’s degrees don’t bring the ideas, choices, and ways of thinking they learn in college back to the towns where they grew up, so the people there don’t hear about them.
The moral and purpose frameworks that religions give people are rudimentary mental health services that work pretty well for most people. But for some people they don’t work at all. In a small farming town where the work is always hard and often dangerous, men need to be strong and keep going to do what needs to be done, instead of acting like women and staying home. So when Billie Joe realizes that he’s gay, and the only homosexuals he’s ever heard of are immoral people in The Bible, he can’t see any good path forward in life.
But it isn’t just him. By the end of the song the events of the story are taking a toll on everyone else’s mental health too.