Earmarks are a modern phenomenon. The founding fathers probably intended a blend of state and federal power sharing, with funding trickling to states if they need it. Congress has authority over federal funding projects and the Founding Fathers intended tax dollars to go towards improvement for ports and overall commerce. Those projects probably led to earmarks in the future.
The founding fathers would likely have recognized that each representative would seek benefits for his region. They may even have desired this to some small extent, as the system inherently recognizes differences between its constituent states. However, the founding fathers were largely suspicious of centralized government and allowing too much power to it. They probably would have looked to the states to handle their own financial needs. Earmarks seem contrary to this.