After you stick with it a while, you'll become more comfortable with it and the pain will subside.
For many people after they start running the muscles around the knee tighten up and better hold the knee in place which makes the knee feel better when they run, which facilitates even more running.
Of course some people have legitimate medical reasons for not running, but I recommend that everyone see a doctor, have their legs checked out, and most likely they'll get the a-okay.
In my opinion nothing can top running, but if you are looking for other cardio excercises, you could give the ole rowing machine a go, or try a low weight/high rep/short time between sets work out like that Randy Couture workout I mentioned early in the thread.
All just my opinion of course.