On the following album, The Times They Are A-Changin', the targets are even more diffuse.  "With God on Our Side" relates a litany of various wars, the Cold War and other historical events – such as the slaughter of Native Americans in the 19th Century and the Holocaust – in the context of the oft-believed notion that God or some other higher power is "with us".  Tellingly, nothing is said about the Vietnam War at all in the song originally, although a verse was added for live performances in the 1980's.  I had never heard that before, and I doubt you had either; here is the added verse:  "In the nineteen-sixties came the Vietnam War / Can somebody tell me what we're fightin' for? / So many young men died / So many mothers cried / Now I ask the question / Was God on our side?" 

(May 2013)

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A bit of serendipity occurred when Bob Dylan and Joan Baez appeared together at the 1963 Monterey Folk Festival singing a duet of a newly written song, "With God on Our Side" (which would appear on Dylan's next album, The Times They Are A-Changin').  The Festival was in the same month as the release of The Freewheelin' Bob Dylan.  Wikipedia states:  "Baez was at the pinnacle of her fame, having appeared on the cover of Time magazine the previous November.  The performance not only gave Dylan and his songs a new prominence, it also marked the beginning of a romantic relationship between Baez and Dylan, the start of what Dylan biographer [Howard] Sounes termed 'one of the most celebrated love affairs of the decade'." 

(March 2015)