In this paper we aim to demonstrate how physical perspective enriches usual statistical analysis when dealing with a complex system of many interacting agents of non-physical origin. To this end, we discuss analysis of urban public transportation networks viewed as complex systems. In such studies, a multi-disciplinary approach is applied by integrating methods in both data processing and statistical physics to investigate the correlation between public transportation network topological features and their operational stability. The studies incorporate concepts of coarse graining and clusterization, universality and scaling, stability and percolation behavior, diffusion and fractal analysis.