Joe,
My first thoughts are "What is the time period?" Is it 4.4 cents per ton per year? Second, is it going to be actual or potential emissions that are regulated. Third, how are the fees going to be calulated (who's going to monitor the emissions).
With respect to your question about why the cars will not be taxed, in general, it is much easier to regulate 20,000 businesses than 100,000 cars because the businesses are immobile.
The Bay Area Air quality district has specific boundaries just like any city or county. It's juridiction extends only to the limits of those boundaries. Think of sales taxes. In Georgia, the sales tax ranges from about 5.5% to 8% depending upon which county you are in.
MikeCJ