You are correct - running is excellent for your overall health. It increases your cardio vascular endurance, strengthens your lungs and heart, helps promote better and more restful sleep, strengthens your muscles and tones your entire body, can help in weight loss, and does wonders to help and improve your mental health (by balancing out depression and worsened moods, alleviating anxiety, helping cope with stress, and by providing a physical release for pent up aggression, worry, and anger). Running can benefit you in SO many ways, but just like most great things in life, there are a few catches.
Running is a high impact exercise. The high intensity component of running is exactly why it is such an efficient calorie burn, why it creates such beautifully sculpted legs, and why it improves your overall heart and lung health - but it can come at a price if you are not careful. The repeated pounding of one's legs on pavement or road can create joint problems over time, particularly in the ankles and knees. Your bones and joints can really take a beating if they are over worked and do not receive adequate rest and recovery. You might have heard of "runner's knee," which is exactly this: repeated pounding on the knee joint and patella can cause bone deterioration and strained knee tendons and ligaments.
To avoid worsening your condition, be sure that you are getting enough rest and recovery, and that you are icing your knees after each run. If you start to notice any swelling, immediately stop running and take several days or weeks off to let the swelling subside and pain decrease. Then, once you think you are ready to return to running, take it show and be sure you are running in shoes that offer enough stability, cushioning, and support. Purchasing and wearing a knee brace or stability wrap may also help decrease patella (knee cap) pain.