Simple answer: don't use manual mode.
I think there's a prevailing attitude among some camera owners that if they're not in manual mode, they're not doing proper photography. Some people seem to believe that professional photographers always shoot in full manual mode, even if they are taking snapshots of their daughter's friend's birthday party, for example.
Neither is true. Manual mode is specifically helpful for when you want to be able to set a particular aperture and shutter speed. If you are not in a specific situation where you want a specific aperture and shutter speed, you don't want manual mode.
When you shoot in full manual mode you are fully responsible for exposing the picture correctly: making it not too light or dark. The camera will not help you at all. If you shoot in manual mode but complain that the picture is too light or too dark, you are putting the cart before the horse: the whole point of manual mode is for when you know how to set the exposure better than the camera would if you let it choose them automatically. Using manual mode should start with knowing what aperture and shutter speed will result in the desired exposure.
What's happening in your situation is that you are using full manual mode but have not taken the care to choose an aperture and shutter speed that would result in a correct exposure.
The long answer to this is to teach you all about aperture and shutter speed and how exposure is calculated.
But the more concise answer, in my opinion, is just to advise you to use auto mode.
Professional photographers venture away from auto mode because they want to achieve a specific effect by using a particular shutter speed or aperture (or both). That is, they understand what effect a particular aperture or shutter speed has on a picture and want to exploit that. It doesn't sound like you're in this position since you expected the camera to get the exposure right.
If you would like to learn more about the effects of aperture and shutter speed, by all means do so. Also check out the Aperture-Priority and Shutter-Priority modes on your camera, as they allow you to have full control over just one of these settings at a time while the other one is adjusted automatically by the camera.