Mubarak's concession created a power vacuum within which an array of competing forces will now battle it out, including still-powerful elements of the Mubarak regime, the broader ruling elites (including the opposition), the military, etc. *Late Update: For a thorough treatment of these competing forces, see this blog post by Paul Amar (thanks to TPM Reader DB for the tip.)
The proximate target of today's violence was anti-regime protestors, but the ultimate goal of those coordinating the violence is to improve their positions in the post-Mubarak Egypt. That's not a defense of Mubarak. It's an observation that there are many competing interests swirling through Tahrir Square.
They may have been "Mubarak's thugs" but with Mubarak gone they will still be thugs, grasping for the brass ring Mubarak has relinquished. Calls from inside and outside Egypt today for Mubarak to do this or to refrain from doing that may overstate the power Mubarak still has to control the events that have been unleashed.