Looking at the data sheet it doesn't look like there isn't a USB-to-UART interface. This would make it easier since you would just setup your C# program to communicate with a COM port.
It looks like Altera is using the JTAG Blaster link as their communications link. This may a little different to setup but I would recommend loading up the Altera project file for their GUI and inspecting the file to see how they do it.
---------- Post added at 11:05 ---------- Previous post was at 11:02 ----------
UART is a standard piece of hardware that manages sending serial communications from say a PC to a embedded device. It manages bringing the serial data, then translates it to parallel data, then the FPGA when the data is ready so it can be read in one read.
---------- Post added at 11:06 ---------- Previous post was at 11:05 ----------
Your serial port on your computer has a UART. Since serial ports have been going away, USB-to-UART is a bridge that makes a virtual serial port/UART over USB. You dont have to deal with overhead of USB protocol you can just deal with it like any other COM port.