Canon still don't have a built-in eyepiece cover for the 5D line like the Nikon D700 - making you use that S___ty little rubber eyepiece cover that might be attached to your neck strap, if you use a neck strap.
It's for light leakage doing low-light long exposures. Star trails, Lee Big Stopper work especially. Read you camera manual about why it's useful, and in some cases required. Similarly it's why we use lens hoods. Not all light is good light.
Have you read the camera manual? I'm guessing no, so you might want to take your own advice. The manual states, "If you take a picture without looking at the viewfinder, light entering the eyepiece can throw off the exposure. To prevent this, use the eyepiece cover...
" What 'throw off the exposure' means is that the metering
will be affected, not the image itself, directly. As others have tried to explain, shooting in manual mode solves this problem - you set the exposure while looking through the VF to compose the shot, then when you step back to remotely trigger, light entering the VF is irrelevant since the exposure will not change in manual mode (assuming you've set your ISO to a specific value, on models which support Auto ISO in M mode).
During the exposure, the reflex mirror (the 'R' in dSLR) is flipped up and completely blocks light entering the viewfinder from reaching the sensor. If your
camera is leaking light during long exposures, you should send it to Canon Service, because light leakage sufficient to affect an image directly means a defective camera.