Do you have an old knee injury or any form arthritis? I have arthritis and I sometimes have severe knee pains, but I workout six days a week. Are you doing only cardio or strength conditioning cardio? The reason I ask because it burns more calories and there are different techniques you can use to relieve the pressure off your knees, but you would have to tell me if the pain is in the front of your knees or the back.
In addition, get some good workout shoes and if you are working out at least 5 days a week you should change your shoes every three months. Also there is this cheap analgesic gel called Ice Blue, it smells a little, but it does wonders for my knees.
Finally, if your knees are not getting any better you may have to see your doctor. It is difficult to exercise when you are in pain. By the way, the treadmill is not good on knees, you may want to work on the elliptical or bicycle, but strength conditioning burns more calories and tones.