See this thread for the full list of FF charges:
http://www.flyertalk.com/forum/dolla...charge-us.html
The FFTRS (Frequent Flyer Tax Recovery Surcharge) of $0.06 per day formerly charged for AA and NW miles was (AFAIK) to cover the excise tax charged for the miles (and may have actually been legally required), while the $0.50-per-day FFS (Frequent Flyer Surcharge) formerly charged for all the other airlines was more of a straight recovery on the fees charged by the airlines to Dollar. These have been renegotiated (only AA mileage earners still get charged the FFTRS by Dollar) to the higher amounts shown in the thread I linked to.
Interestingly, though, the dollar amounts of the surcharge are not really tied to the fees Dollar pays. From what I understand, Dollar locations pay around $5 per transaction to DTAG HQ's loyalty program account, regardless of the amount of miles given or length of rental. Therefore, a Dollar location loses money on short rentals and makes money on longer rentals (depending on the program being credited to).
I'm very unclear on the details of how this all works, though, because I've been given conflicting information about it all. I could be entirely wrong and it could be a straight pass-through charge.