Because in California, when they're running away they're no longer a threat to your life... or something like that. The law here only does something when the perp comes back five times to mess with you, perhaps killing you in the process.
That's almost universally true. As a general rule, deadly force is only legal in response to a real imminent threat. Someone running away probably wouldn't be considered such a threat.
There are some exceptions, and Texas does allow the use of force to recover stolen property from a fleeing robber. But California, uniquely, allows one to pursue a deadly threat if necessary.
Still, the clerk could find himself in trouble if there was a hostile prosecutor. It sounds like the robbers didn't have time to steal anything, and shooting at the car as it was driving away isn't usually considered self-defense. But more than likely the authorities will be sympathetic.