The ideal method to discourage air pollution is to charge air polluters an amount proportional to the pollution they produce. There are different factors in automobile and truck usage that relate to the amount of pollution produced, and can be approximated by different charging methods.
Vehicle ownership. Owning a vehicle has some constant pollutants, such as CFCs. Significantly raising the vehicle registration fee would especially discourage clunker cars (the least safe) and teenagers from driving.
Emissions fee. Measure the pollutants from an automobile, similar to what is presently done, but on a yearly basis. Multiply by the vehicle miles travelled (VMT) of that vehicle by using the odometer. Do not exclude trucks, buses or motorcycles.
Vehicle trips. Just turning on the engine causes much of the air pollution. A charge for vehicle trips is accomplished by a counter (with a 10 minute timer so that re-starting engines would not be counted). The annual emissions inspection would record the count.
Fuel tax. In California, the petroleum industry produces more hazardous waste then all other industries combined. (Source: Citizens for a Better Environment). A fuel tax encourages conservation and is one of the easiest to administer.
Noise pollution. Measure decibels for trucks, motorcycles, buses and vehicles with snow tires. Noise above a certain amount, measured while traveling at a certain minimum speed (for tire noise), and accelerating from a stop to a minimum speed (for engine noise), should be charged a rate times miles driven.
Rubber dust. About 4 pounds per car per year (average) are removed from tires as "rubber dust". This is, in fact, a toxic petroleum product that also creates a yet-unresolved environmental disposal problem. Charge a fee on tires based on tire width, vehicle weight, and/or other criteria. Do not exclude trucks or buses.