I think that you're incorrect and that there are probably many court cases that would suggest that employees must be permitted accomodation for their religious practices.
Additionall I think that if any employer tried to ban me from having my Bible, Koran, Book of Morman, etc in my car that they'd be in trouble.
So why should the Second Amendment be any different?
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.