If you were judging by the song's name and it's rousing chorus, you would think that "Born in the USA" was an anthem proclaiming the glories of being an American. If you take the time to listen to the lyrics though, you'll find it is more complicated than that.
Springsteen's song is actually a narrative about the hardships of being a Vietnam veteran. It starts out describing the protagonist's working class roots. It then discusses his time in the armed forces and concludes with his difficulty upon returning to America. The song protests the poor treatment of Vietnam veterans when they came home from the war.
Scholars have also theorized that the song is a testament to the American working class. It laments how economics and politics failed to protect this class during the 1970s and 1980s.