We would appreciate if you can make the following changes to your VMware image (tested on base operating system as Windows with VMWare server but should work on other platforms):
1) Open the .vmx file of your Windows/Linux VMware image in your favorite text editor
2) Add the following line at the end of the .vmx file:
usb.generic.allowHID = "TRUE"
3) Save the .vmx file and start the Windows/Linux VMware image
Now, the Windows/Linux OS installed in VMware will start recognizing the YubiKey.
Also add a USB controller using the VMware Server Console. You can add the USB controller by selecting the Windows/Linux VMware machine's settings and clicking on Add button under the Hardware tag.
Whenever you insert the YubiKey in the physical server running the Windows/Linux VMware image, using the VMware Server Console you need to click on VM --> Removable Devices and select the YubiKey. This will enumerate the YubiKey in the Windows/Linux OS running under VMware. Now hopefully you should be able to use the Windows/Linux personalization utility to reprogram your YubiKey.
We hope this helps!