Modern wireless technology opens the door for several new Intelligent Transportation applications. In an academic environment, students use transit bus system on a daily base. El-Tawab et al.  introduced a cyber-physical system to monitor the quality of service for transit buses around an academic campus. This cyber-physical system detects the number of riders waiting for the bus system at each bus station and number of riders on each bus. In this paper, we examine the security and vulnerability of the bus data collection system and provide remedies. Smart units are used to collect data (e.g., Media Access Control (MAC) Addresses) to uniquely identify students' smart phone waiting times for the bus at each station. The goals of this system are to identify the average waiting times at each bus station, route optimization and dynamic routing. Several security concerns occur with the collection, transmission, and storage of data in the Cloud (e.g., Man in the middle attacks, unauthorized access, denial of services, theft, etc). We analyze some of these cyber-attack vectors and provides mitigation techniques, cyber hygiene best practices, and suggest ways to balance security versus convenience.