The administrative charge for rental car tolls has been discussed on here before. I'm among those who agree with you that it's an outrageous fee for a pass-through charge, but there are those who defend it as a reasonable charge to cover the administrative costs associated with this.

That said, in your case, I would contact Thrifty to ask them to remove the toll charges. Do not focus on the fairness of the $15 fee, as that's a separate discussion. Rather on the fact that you did not incur the fee in the first place. If Thrifty does not promptly remove the charges, then dispute the charge with your credit card issuer. Just my two cents.