Is there a difference in landing fees for charter and scheduled flights?
This is almost completely dependent on the airport but we can talk somewhat generally. 

For what its worth airlines (scheduled carriers) can often negotiate lower landing fees by being able to guarantee a specific amount of flights into an airport. Charter companies don't have this luxury since it can be hard for them to predict where and when they are going. On the other hand some fees are set by the local government, for example here in Philadelphia any airport in the city (KPHL and KPNE) has landing fees set by the city. You can find the official legislation here and I assume thats non negotiable but I cant be sure. 

There is also a bit of a discrepancy due to the type of planes. Landing fees are often charged by weight and in most cases charter planes are flying smaller stuff than the scheduled carriers and their fees may be lower as a result (even though the scheduled carrier has a lower rate). If we look again at Philadelphia we can see that they have fees for both weight and passengers which generally go hand in hand however a charter company may be flying a big RJ for just one guy while a scheduled carrier may be operating the same plane at its maximum seating arrangement. 

Charter carriers may also have the luxury of flying into smaller satellite airports where the fees may be lower or structured differently. Since some of these airports could potentially be private or private/public they have the ability to charge what they chose. Some will even have no fee if you buy a pre prescribed amount of fuel. 

For other points of reference you can check out the 


New York Landing Fees
Miami Landing Fees