Because there are safety issues involved.
Private property restrictions on the First Amendment aren't really threatened by something someone keeps in their car. If an employee, fired or otherwise, retaliates by going to his car and bringing in his issues of Hustler or the Watchtower it won't be very hard for HR to clean up the mess quickly and undo the violation of their policies.
A gun in the car has the potential for exponentially greater damage. Yes, most everyone who keeps a gun in the car is a good gun-owner, but the liability caused by the exceptions is what private property owners have to consider. And it's unfortunate, but getting fired, particularly under bad circumstances, can turn a really large percentage of otherwise sane people into exceptions. Companies don't want to risk it.
Bogus argument and insulting to gun owners.
Employee safety is not threatened by guns inside cars.
Those who are likely to take hostages and commit murder are not likely to be deterred by company policies against having a firearm in the parking lot or in the workplace proper.
Now your argument works both ways; that copy of Hustler (Odd how you threw pornography into the mix!) or Watchtower won't protect the car's owner once that car leaves the parking lot.
So if this is really about safety, your argument misses the mark.
You'd disarm all because you think that maybe one might some how someday commit a criminal act.
Are you also going to ban scissors and pocket knives and hatchets from cars?