John Prine has a few great ones including
rape of the environment: "Paradise"
Vietnam war: "Your Flag Decal Won't Get You into Heaven Any More"
drug laws: "Illegal Smile" (I don't know if this is really a protest song or just a character study of a druggie)
And of course Arlo's daddy wrote his share: "I Ain't Got No Home," "Do-re-mi," "Hard Travellin'," "Deportee"--and on an on
Others worth mentioning: Billie Holliday's Strange Fruit, Buffy Sainte Marie's "My Country 'tis of Thy People" (my nomination for the most passionate solo protest song performance ever is Buffy singing this song) and "Isaac Hayes"
Some old timers: "Darling Nelly Gray," "John Brown's Body," Joe Hill's "Pie in the Sky," "Wearin' o' the Green," "No Irish Need Apply," "Get Back," etc.
A recent one by Si Kahn, recorded by Hazel Dickens and by the Dry Branch Fire Squad--about the loss of jobs to wherever: "Aragon Mill"