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

Answer: 
ClickOnce cannot install a driver.

ClickOnce simply copies files from a server location to a client's profile and keeps them in sync. The main reason people get confused is because Visual Studio does extra stuff when you use it to deploy. It creates both a web page and a bootstrapper for prerequisites. The bootstrapper bundles all your prerequisites into a single package but is totally separate from ClickOnce.

You could include your driver in the bootstrapper, but users are ultimately responsible for deciding whether or not to run the bootstrapper before your ClickOnce app. Another option would be to use ClickOnce to deploy the driver file and then write custom code in your application to install it. This assumes your application is able to start without the driver installed and that the user has enough privilege to install the driver.

If you come up with a working solution, please follow up.
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.