Don't listen to the last two replies. Those are absolutely the wrong way to look at how you should pay fees or negotiate dealer documentation fees.
Dealer fees include, Taxes, license, registration, smog, and documentation fees. In almost all states, taxes are collected from the customer and then given back to the government. The dealer only acts as a middle man for that process and gains nothing out of it. License & registration fees are based on a percentage of what the Department of Motor Vehicles for your state calculates. Depending on what state you live in, smog fees are collected from the consumer, because smogs must be completed as the process of registering a vehicle to a new buyer.
The only fees of these that were stated that could possibly be negotiable are the documentation fees. These are collected by the dealer to pay for all the forms and paperwork associated in purchasing a vehicle. California has a cap of $55 for this charge. Considering the amount when negotiating the price of a vehicle, that fee of $55 is negligible.