I can't say what was the motivation of the original authors, who apart from Leavitt were motivated by graph C*-algebras which in turn were motivated by symbolic dynamics. From a Computer Science point of view it is quite natural. Let's assume the digraph is finite and has no sinks or sources for convenience.
Imagine you store an infinite path in your graph on a stack. You have the operations of pushing your favorite edge onto the front of the path on the stack or popping your favorite edge from the front of the path when these operations are defined. You can build from these operators on a vector space with basis the infinite paths in your graph by interpreting an undefined operation as sending a path to 0. It is easy to check these operators satisfy the Leavitt path algebra relations and under mild conditions generate a copy of the Leavitt path algebra.