Of the people mentioned so far, my favorite is Dylan, hands down. But I'm sure he would object to being characterized as a "protest singer," and I would agree with his objections. In fact, the term "protest singer" is such a confining category that I think any good songwriter would probably object to being put in that box. Most of Dylan's best stuff had little to do with politics, and some of his political stuff was pretty lame in my opinion (including some of the "big hits" like Masters of War, With God On our Side, etc.).
In this context I tend to think more of songs than of singers. Seeger's "Big Muddy" has to be on the short list of truly great political songs of the 60's, as do Tom Paxton's "Lyndon Johnson Told The Nation" and Joe McDonald's "Feel Like I'm Fixin' To Die Rag". But I don't care for very many overtly political songs from the 60's; in my estimation most fall short musically, or oversimplify the political issues, or both.
Just in case there's somebody left out there that I haven't pissed off, I also have to say that I've never heard anything by Phil Ochs that impressed me. I'll take it on faith that he was sincere, and I'm certainly sorry that he died as young as he did, but in my opinion he was not much of a songwriter, and a pretty middling singer.