Nearly all receivers are this way. The reason is, the m/c input is supposed to be already processed by the source.
If you use a digital connection for DVDs (assuming it is not a high def player) you should be able to use your tone controls. In other words, if you are not using a high def player and you have digital connections, you don't need to use the m/c inputs. Ideally, with a well calibrated system, you should not be messing with the tone controls at all once you find a setting that works.