I'll be honest with you, I don't know if Antifa has their own website or their own twitter, but not once have I seen them order a group of masked individuals to beat up people at Milo's event.
I'm assuming that the masked individuals who did beat people up were acting on their own as their own collective, and even though they identify with Antifa they were not directly ordered by some central power to carry out their actions. The rioters should be charged with crime, not the movement that they follow.
The 'expression of free speech' i keep referring to is their loving movement, not the national socialist punchers or masked men who decided it was alright to physically abuse others for their beliefs. Antifa as a movement is not dictated by these violent individuals. If they were, i'd be all for labeling them a terrorist group and supporting their immediate shutdown.