It's worth mentioning that the petition acknowledges the need for additional taxes, and every pilot I've talked to agrees that an increase in existing tax revenues would be preferable to adding the infrastructure, bureaucracy, and overhead needed to collect a $100 fee for ATC interaction.
In case you're interested, Here's Obama's proposal:
Here's the exact text proposing "User Fees:" (pp. 22-23)
More equitably share payments for air traffic services.Roughly two-thirds of the air traffic control system’s current costs are financed by aviation excise taxes. Most of the tax revenue is collected from commercial aviation through ticket taxes, segment fees, international head taxes, and fuel taxes. General aviation users currently pay a fuel tax, but this revenue does not cover their fair-share-use of air traffic services. All flights that use controlled air space require a similar level of air traffic services. However, commercial and general aviation can pay very different aviation fees for those same air traffic services. For example, a large commercial aircraft would pay between $1,300 to $2,000 in taxes for a flight from Los Angles to San Francisco while a corporate jet flying the same route and using the same Federal Aviation Administration (FAA) air traffic services would pay about $60 in taxes. To reduce the deficit and more equitably share the cost of air traffic services across the aviation user community, the Administration proposes to establish a new mandatory surcharge for air traffic services. This proposal would create a $100 per flight fee, payable to the FAA, by aviation operators who fly in controlled airspace. Military aircraft, public aircraft, recreational piston aircraft, air ambulances, aircraft operating outside of controlled airspace, and Canada-to-Canada flights would be exempted. The revenues generated by the surcharge would be deposited into the Airport and Airway Trust Fund. This fee would generate an estimated $11 billion over 10 years. Assuming the enactment of the fee, total charges collected from aviation users would finance roughly three fourths of airport investments and air traffic control system costs.