How do you charge your customer in a project using agile methodology?
Per hour? Then a great deal of trust has to been established before the project.
Per iteration? There's gonna be a lot of budget decisions, which can take time.
Per project? How can you do that when you don't know the scope? The very essence of agile is to not write a big upfront design/specification.
You charge your customer on the base of the terms defined by your contract that will be slightly different from a traditional fixed bid contract. Let's call that an Agile contract.
Some options are discussed by Alistair Cockburn in Agile contracts.
Another great resource is 10 Contracts for your next Agile Software Project by Peter Stevens.
Mary Poppendieck also has great material on this topic. See agilecontracts, agilecontractsworkshop, Contracts Excerpt From Lean Software Development, Lean Contracts. More here.