The case against violence
It's a question on which I personally haven't yet come to a conclusion. Both sides have legitimate points to make. Again, it's about dealing with extremist and dangerous groups, not the "ordinary" opposition. This was terrorism; doing the same to the local KKK headquarters would be a more debatable act.
In this post, David Neiwert makes a powerful case for the anti-violence side of the argument. It's long, but worth reading if you want to debate the issue in an informed way. He makes the important further point that we have other weapons far more effective than violence, and those should be preferred even if you don't find violence morally troublesome.
I would make one final point of my own, not so much about our view of anti-fascist violence as about our judgment when some do commit it. Never forget the magnitude of the provocation. Confronting a Jewish person with swastika armbands, or confronting a black person with a Confederate flag, can fire up feelings of an intensity not easily understood by people who have no such horrors in recent historical memory. These issues are not just abstractions. Always remember that.