Frequently our patients ask us this question in one form or another. The very short answer? Yes. And no. I'm sure there are authorities in plenty of health professions that will heartily disagree with my following explanation, and they are welcome to. I'm simply sharing what has been my personal and professional experience in my career.
Ideally, our knees were created to function optimally throughout our lifetime. Our knees were not designed to carry excessive weight, (ask any of your pregnant friends), they were not designed to be used in a state of dehydration, they were not designed to have to work with less than sufficient nutrients specific to the knee joint- i.e. chondroitin, glucosamine and other pro-cartilage nutrients. So all these conditions being met, and baring other traumas, (rugby accidents, soccer injuries, skiing- well you get the idea) no, running shouldn't be bad for your knees. If we had wonderful living conditions and we all drank water only when we were thirsty, ate fresh (not over-cooked, canned, fried or otherwise ruined) produce and great source of protein every day, (I'll leave the vegan vs. carnivore question for another day) our knees, again in theory, should hold us up for as long as we need them. This also is not accounting for environmental effects that cause degeneration in all types of our tissues. We leave that discussion for another time as well.
Conversely if you are signifigantly overweight that alone is enough to put a lot of wear and tear on your knees, if you add dehyration to that equation (most of the population lives in a state of low-grade, chronic dehydration) you're just asking for trouble, and if the tissue in and around the knee doesn't have enough of the right 'construction materials' read, nutrients here, to rebuild the tissue at night while we are supposed to be resting, well then the joint continues to degenerate over time, rather than staying healthy and functional for us. Yes, running can be bad for your knees.
The final answer is this: Take care of your knees, and they'll be there for you.