As noted above Rage Against the Machine was 100% protest material, it's a real shame they broke up (Audioslave is not even close to what RATM was). I woulda loved to have seen RATM live *sigh*
Although I can't tolerate most rap music it should be considered protest material, rallying against inner-city issues such as poverty, gang warfare, etc. There's also the infamous "cross-over" bands e.g. Limp Bizkit (but it's easy to doubt their sincerity). Oh, Green Day's American Idiot takes a stance albeit it their issues seem to be primarily with GWB.
In my mind the big difference between protest music in the 60's and the stuff that has come out since is primarily in how it's delivered. The 1960's was peace & end the war, for the most part delivered in a folk song meant to appeal to your intellect and compassion. Bruce Cockburn kick-started a new generation of protests with more in-your-face lyrics ("Call it Democracy", "If I Had a Rocket Launcher", "People See Through You", "The Trouble With Normal", etc...) but added a little harder edge to the tunes. If you get a chance read Cockburn's lyrics, he's a brilliant song writer. Midnight Oil followed a similar vein, Peter Garrett was very much in tune with world issues and made a point of speaking his mind. Treatment of Aboriginals, corporations abusing the land for profit, superpowers acting as the world's conscience... Midnight Oil covered it all. In fact Peter is now "walking the walk" as a member of Parliament in Australia, doing his part to effect change. Midnight Oil was an awesome band live, gonna miss Pete and his antics.
To sum it all up protest tunes have been delivered a LOT more forecfully in the last 20 years than ever before (and cover a wider range of issues), there's a lot of anger out there folks.