the COM port is a DE-9 (it has 9 male pins on the motherbard) serial interface used for data transfer, and is often included for legacy support, though there are still numerous peices of hardware that use it today.
To disable this in Windows, access your device manager (right click my computer, click properties, click the hardware tab, then click device manager), Scroll down to the ports list (often after the network adapters). expand the ports list, and COM 1 should be visible there. Right click COM 1, and select disable. It will ask you do you really want to disable it, and click yes.
The COM port can be disabled in the BIOS, but this is usually a per computer basis.