To use the
Windows 7 USB/DVD Download Tool, you will need to first ensure that you have access to an ISO image file of your installation media. Once you have an ISO file of your installation media, you can simply run the tool, which will ask you to point to the .iso file, and have it create bootable media on a USB device. The Windows 7 USB/DVD Download Tool is only compatible with Windows installation media. The Linux distribution you mentioned may have an entirely different boot process which is incompatible with the tool.
Lastly, one of the most common errors with installing Windows from a USB stick on many modern systems is the use of a USB 3.0 port. The drivers for these ports are not present in the setup environment on the installation media and thus the boot files are not detected. If your media has been created correctly using the Windows 7 USB/DVD Download Tool, you may simply wish to try it in a USB 2.0 port.
Beyond what was described above, an alternate method for creating installation media for your system would be to use the deployment technologies available from Microsoft for administrators and IT professionals to deploy large quantities of Windows to systems in an organization. The
Microsoft Deployment Toolkit (MDT) installed on another workstation would permit you to import your installation media and create a customizable installation interface on a USB stick. Furthermore, it offers the ability to automate installation of applications, configure settings, automatically install drivers both in the Windows Preinstallation Environment (Windows PE) and in the deployed operating system, and quite a bit more. With a Windows Server with Windows Deployment Services (WDS), it even supports PXE boot where you could boot your PC directly from the network with no local media and perform the installation directly over the network from the Deployment Share.
For more information on deployment technologies offered by Microsoft, check out the video
Alphabet Soup Deployment: Understanding MDT, WDS, MAP, ACT, SCCM, and USMT. The
Windows 8 Deliver and Deploy page from the Springboard Series on TechNet provides even more information including guides for using the various deployment technologies, videos, walkthroughs, and more.