We only charge for what is used... but we are a road house so it is a different game. However, if we sub in backline and the drummer shows up with a kit they promoter still eats the cost because we payed for it. We do charge different levels for different levels of production, if you want our full monitor rig, FOH rig, racks and stacks, and all of our mics you get one rate vs a podium/mic talking heads thing. It is all still there, but you don't have to pay for it. In our place paying the rental fee for the hall includes nothing, we cost account for everything from PA to flooring to backline.
I guess it really depends on how you are set up. If every show is custom and you pack the truck every day for a different event then charge for what goes into the truck. If you are one of the operations that operates on more of the film grip truck model where everything lives in the truck, then charge for what is hauled out of the truck.