The goal is to generate more income and not less, so you need to set up a system that provides for that. You can abstract out the core of the project, set a fee for that and tack on hourly rates for things outside the initial scope. You have to be careful in how you do things but it should ultimately lead to more money.

If you're happy making $x/hour or whatever then by all means continue to do so. If you're looking for more, you may want to start exploring other billing models.