Fly.io, a platform that runs container images on hardware around the world, uses WireGuard as a fundamental component of its infrastructure. The company developed a user-mode WireGuard implementation that allows users to access their applications without requiring root access. This implementation has enabled features such as SSH access and remote builds, but has also presented challenges such as slow peer creation and potential connectivity issues. The company has made improvements to its implementation, including reducing the time it takes to create new WireGuard peers.