What are the various fees associated with flying?
I will answer this for the US as that is the jurisdiction I know best. 

There are no airspace or ATC usage fees here in the US. The airspace and its resources are free for any plane of any size that conforms to the FAA's FAR's and is legal to fly in a given airspace. 

The FAA is in the process of adding overflight charges for aircraft that fly through our airspace but neither land nor depart from the US.

The only fee (somewhat indirectly related but not a component of the airspace its self) is for planes coming in from abroad who will need to pay some customs fees to enter the country.

Strictly speaking you may be required to carry IFR charts or VFR charts on board to conduct the flight in question in US airspace. These must be purchased from an official source. The FAA maintains them but the Pilot must pay for them. Until recently the FAA also physically printed them and they were purchased directly from them but this is no longer the case.  

If you extend the question to include airports the answer will drastically change for the US.