First of all, the risk in an individual encounter is so small for a civilian that fear of being shot is irrational. Furthermore, if the civilian wants to reduce his risk even more, probably by at least a factor of 10 (to bring it down below the risk that the police officer faces), he can do so by being compliant.
Second of all, and more importantly, the police officer is not acting out of fear. He is acting according to an established protocol, which has been designed to minimize his risk in any individual encounter because he is expected to face many, many such encounters over his career, and it would be untenable to allow the risk in one such encounter to be higher than a certain very low limit.
It is the same reason that an airline pilot goes through a ridiculously long checklist before taking off or landing. He doesn't do it because he's afraid that the plane will misbehave at a critical moment on any particular takeoff or landing, but because if he doesn't go through the checklist every single time, then the risk is unacceptable over the long term.