Containers enable high performance and easy deployment due to their lightweight architecture, thus facilitating resource utilization in edge computing nodes. Secure container runtimes have attracted significant attention because of the necessity for overcoming the security vulnerabilities of containers. As the runtimes adopt an additional layer such as virtual machines and user-space kernels to enforce isolation, the container performance can be degraded. Even though previous studies presented experimental results on performance evaluations of secure container runtimes, they lack a detailed analysis of the root causes that affect the performance of the runtimes. This paper explores the architecture of three secure container runtimes in detail: Kata containers, gVisor, and Firecracker. We focus on file I/O, which is one of the key aspects of container performance. In addition, we present the results of the user- and kernel-level profiling and reveal the major factors that impact the file I/O performance of the runtimes. As a result, we observe three key findings: (1) Firecracker shows the highest file I/O performance as it allows for utilizing the page cache inside VMs, and (2) Kata containers offer the lowest file I/O performance by consuming the largest amount of CPU resources. Also, we observe that gVisor scales well as the block size increases because the file I/O requests are mainly handled by the host OS similar to native applications.