Protected mode is the 286 backwards compatible architecture state the processor goes into while in DOS. If I remember correctly anyways. Most BIOS updates recommend going into "Protected Mode" (basically boot off of an old bootdisk or something if you have me/2k/xp) for flashing the BIOS. If the thing you have is just a driver, you don't need to worry about it.
If the file you have is a .zip, extract everything and see if you can find a .inf file in it all. If so, you can rightclick it and choose the "Install" option.