'Masters of War' was not about the Vietnam War - - it was about ALL war and those who profit from it (the defense industrial complex that Eisenhower warned about in his farewell speech?). The song was included on Dylan's Freewheelin' album which was released in May 1963 (Kennedy was President!) and Vietnam was just coming onto the radar screen.
Now that is quick information. He converted to Christianity I believe in the late 50s early 60s and the references and allusions start to make a heavy presence.
Bob has said it isn't an anti-war song. It's an anti-war- profiteering song. Marine General Smedley Butler, who wrote the great book "War Is A Racket", would have liked it.
Bob's songs were more about right and wrong and being clean and decent than about irresponsible sex and drugs.