The reason FAA has the concept of commercial operating certificates is so that:
a) it can make sure those operators are following regulations enacted for safety reasons.
b) It can revoke the certificates of operators who for one reason or another violate those regulations.
The FAA has very little authority over an entity (person/corporation) who operates without a license or operating certificate. (I think it can levy fines against individuals but I'm not sure where their authority stops in that sense. I don't believe the FAA can act in a law enforcement capability, so it's not clear to me at what point a person can be arrested for violating FAA regulations).
By licensing drones, the FAA can enact rules to prevent them from endangering manned aircraft. For instance, if something akin to a type certificate is required by drones because FAA finds that certain equipment (like ADS-B) is required to insure separation from manned aircraft, how would they enforce that? Probably the way they will is by having certain equipment requirements for drones that want to operate in the national airspace.
Hopefully they will use a layered approach so that very small light drones will have little to no equipment requirements, but may have severe altitude restrictions, while larger/heavier drones, or drones that need to be operated at higher altitudes will have equipment requirements to keep them separated from manned aircraft.
We also have the issue of parts falling out of the air onto the public. In general this isn't an issue for manned aircraft, because usually when big pieces fall off the aircraft, the people on board are killed - it gives the crew plenty of incentive to make sure this doesn't happen. But what's to prevent an SLR carrying drone from falling out of the sky and killing people walking down the sidewalk? Since there's probably little to no risk on the part of the drone operator, we need a way to enforce some rules about how drones can be operated above people...