automotive project
If you are referring to the Xilinx/Digilent Spartan-3E Starter Kit, then its USB port is connected only to the FPGA's JTAG configuration/debug port. Unfortunately, Xilinx refuses to provide documentation for their USB protocol, so you have to use Xilinx software, and the only software they provide that can do general-purpose JTAG communication is ChipScope's TCL interpreter. You could write a ChipScope TCL script that talks through USB through JTAG to a BSCAN macro and scan chain that you've placed into your FPGA design, but that's so clumsy!
Xilinx's PDFs also omit the USB page of the schematic, and hide the USB section of the gerber plots (easily unhidden with Acrobat).
I've read some forum discussions about reprogramming the Xilinx USB CPLD with different code that's well documented, so you could talk to it from any USB controller. But remember that you are still going through JTAG, and that's somewhat clumsy. Also, Xilinx iMPACT won't work anymore until you restore the original CPLD code, and reprogramming the CPLD is slow.
I've been searching for a way to get through the Xilinx CPLD without reprogramming it, but I haven't found any clear reports of success.
The Xilinx Platform Cable USB device (XPCU) has the same situation.
If anyone knows an easier way, please speak up!