The aviation industry will face a lot of challenges and when it comes to implementing the user fees at airports. The first challenge will be the allocation of costs on a pro-rated basis. The first most obvious negative effect of user fees is that general aviation pilots--seeking to reduce their cost of flying--will use ATC less. Some of these IFR flights will become VFR flights, flying under the clouds with small or no margin of safety at all.
The second negative effect is that it is inevitable; the decreasing use of ATC services as major general aviation pilots look to reduce their cost of flying and decreasing revenues collected from user fees. Normally when the government finds that fees are not covering costs, they simply have to raise the fee; this would lead to a bad cycle of rising rates and costs for pilots.
The government has now an allocation in the budget for 2011, implementation on user fees. Pilots should remain vigilant and wary for all new attempts to re-implement user fees in new ways built to make them more appealing and more likely to get passed by Congress.
The most effective way for the government to overcome some of the FAA cost is to look at what has worked for several decades. Fuel tax has been effective and most private jet charter companies would accept a slight increase in the fuel tax before user fees would be acceptable.