Question: Can you install a hardware driver, built using WinUSB, along with a C# application deployed using Click-once?

Answer: 
See the following discussion: <http://social.msdn.microsoft.com/Forums/en-SG/winformssetup/thread/51f897d9-a84c-49a6-9305-df9e19986918>

It would appear that the recommended practice is to create a setup prerequisite for the drivers, then include that prerequisite in the clickonce for your app's properties.
Drivers can be uninstalled. My ClickOnce apps deploy the driver files locally on install, then my app checks to see if the USB device is present and if the drivers have been applied. I think this is best, because the user gets the correct error for their situation. If the drivers aren't there, I prompt the user and runas or simply run the installer.