Cells aren't the big problem because they take orders and get their financing from their leaders like Bin Laden. I'm aware of al Qaeda not being a major player in Iraq at the time we went in, but they were their (remember Zarqawi) and were our main combatant before Iran entered the picture and enflamed the sectarian violence that is currently creating the chaos.
If you research State sponsorship of terrorism you'll better understand what we're up against in the war on terror. It's not just al Qaeda or Hezbollah or any other rogue group that we must deal with.
I believe the gangs of Chicago analogy is off the mark. Afghanistan, Pakistan, Somalia etc. etc., these countries have no rule of law to deal with the problem. I agree that relying on our military alone is not a long term solution, but it does have its purpose.