Dylan was very much a war protester before his motocycle accident in the summer of 1966. That event and his long recuperation changed a lot of things about Dylan.
Check out this article—you may or may not agree with it.
http://www.weeklystandard.com/Content/Protected/Articles/000/000/012/727xwxao.asp?pg=2
Heres another interetesting look at Dylan and Viet Nam—
worth a look.