Hertz offers an add-on product called Personal Effects Coverage (PEC) that would have covered this type of loss. If you don't have that, then you'd need to rely on your credit card and/or personal auto insurance. It sounds like your credit card company already said you were not covered, so you'd need to see if your personal policy covers items stolen from a vehicle.

As for the damage to the car, you'd be liable to Hertz unless you took their LDW. If not, then your credit card company and/or personal insurance would likely cover. You would (most likely) need to pay Hertz for the estimated damage and them make a claim to your credit card and/or personal insurance carrier.

As for Hertz's responsibility here, don't hold your breath. Here are a few posts from our blog you may find helpful/interesting:

What Happens if my Rental Car is Vandalized and My Possessions Stolen?

San Francisco Continues to Experience Thefts from Cars, Has No Idea on How to Solve the Problem

San Francisco's Lawmakers and Lawyers Enter the Rental Car Fray, Reveal Dysfunction