JetPack is actually a front end to other software, and other than downloading and running other software, does not actually participate in flash. If not for extra package installation you probably wouldn’t need JetPack. The rootfs directory, and flash.sh, are part of the “driver” package. This is the first thing downloaded for a flash. The driver package has an empty subdirectory, the “rootfs/” directory. Without the driver package there is no empty “rootfs/” available. Basically, when this works correctly, then you will have a subdirectory of “Linux_for_Tegra/” and “Linux_for_Tegra/rootfs/” which later gets filled in with the sample rootfs and some NVIDIA drivers. You are missing the driver package.
JetPack has a manifest file with various URLs for download and unpacking. Either the manifest could not be downloaded, or the manifest referenced the driver package in such a way that the network did not have access to the download. Does your host have complete internet access? Is the host behind any kind of firewall or proxy?