Quantum computing is a newly emerging computing environment that has recently attracted intense research interest in improving the output fidelity, fully utilizing its high computing power from both hardware and software perspectives. In particular, several attempts have been made to reduce the errors in quantum computing algorithms through the efficient synthesis of quantum circuits. In this study, we present an application of an optimization model for synthesizing quantum circuits with minimum implementation costs to lower the error rates by forming a simpler circuit. Our model has a unique structure that combines the arc-subset selection problem with a conventional multi-commodity network flow model. The model targets the circuit synthesis with multiple control Toffoli gates to implement Boolean reversible functions that are often used as a key component in many quantum algorithms. Compared to previous studies, the proposed model has a unifying yet straightforward structure for exploiting the operational characteristics of quantum gates. Our computational experiment shows the potential of the proposed model, obtaining quantum circuits with significantly lower quantum costs compared to prior studies. The proposed model is also applicable to various other fields where reversible logic is utilized, such as low-power computing, fault-tolerant designs, and DNA computing. In addition, our model can be applied to network-based problems, such as logistics distribution and time-stage network problems.