There's 3 main questions that are asked.
1. Is running bad for the knees?
2. Is running on hard surfaces bad for the knees?
3. Is running without cushioned shoes bad for the knees?
These are all basically, variations of the same question. Is impact bad for the knee joints?
Short answer - No.
Long answer - read on.
Impact is not bad for the skeletal system. The result depends on the dose. Both poison and medicine, is in the dose.
The humans are designed to get stronger after every challenge. It depends on the challenge being appropriate for your current capacity.
Nowhere is this more spectacularly demonstrated than in the musculoskeletal system. If you train sensibly and consistently, you get stronger with each visit to the gym. Large increases in the beginning, and smaller increases as you get closer and closer to your genetic potential.
The same goes for running. Each stride you take is an opportunity for the bone, muscles and joints to remodel to become stronger for your next run.
Provided you've recovered from the biomechanical and neurological stress of the previous run / workout.
If you run regularly with good form, without any chronic aches and pains. You end up getting stronger bones, joints, muscles, tendons, ligaments and cardiovascular system.
If you run with bad form, you place load on areas that are not designed to take impact and you end up with an injury. That injury might show up gradually or happen out of blue. However, even if it appears like it's come out of the blue, there's usually a long history of neglect before an injury actually occurs.
Not being aware of the niggle, or trivialising it for long enough, will let your mind ignore it, till it is too late.
Running with good form, and taking accurate feedback from your body, starts with the feet.
And in this respect, wearing the modern running shoe is actually a handicap, in the long run. Wearing shoes, while trying to get feedback from the ground would be like attempting to perform fine surgery, or embroidery, while wearing boxing gloves.
Going barefoot is a good idea to train your feet. Provided you run at a pace, for a distance, that your untrained feet are capable of. And they'll tell you, what they are capable of. If your feet hurt, you need to slow down. Taking your shoes off may show you the problems with your gait, in the form of localised pain in the feet itself. But, because you've bandaged the feet up in your shoes, and you're not receiving the feedback on your feet, the impact ends up causing problems higher up the chain. Your chronic knee, hip, back and even shoulder injuries may have roots in your shoes.
Gait and stability problems that could have been identified early, at the level of the feet themselves, now get a chance to slip past that first line of defense and run rampage in your knees hips and back. Ironically, the first line of defense, your feet, are also the most resilient and the fastest to recover from repetitive loading. Smaller bones in the extremities heal faster and remodel better than the larger bones around the knee and hip.
When it comes to choosing running surfaces, it is counter intuitive. You might think that a softer surface, like the beach is the best. It isn't. The soft sand will not provide much of a rebound as you try to push against it. Your feet will have to work much harder to produce a decent amount of ground reaction force. This usually ends up causing rather severe foot pain and soreness the day after your sprints on the beach. For the same reason that there is far less ground reaction forces in play, you may find that the hips, knees and back find the sand a lot more comfortable. This is also partly due to the fact that you can't run very far on sand.
A hard surface is not intrinsically bad for your knees. It's the way your body absorbs the main force of the impact, that decides where there's going to be wear and tear. On a hard surface with minimal shoes, your feet will start to complain long before your knees get damaged. Thereby protecting you. Plantar fascitis and tendinitis are preferable to premature osteoarthritis.
My basic point is this.
You need to let your feet get stronger. You need to pay attention to the signals you're getting from them. And for that, you're going to have to slow down, get more mindful about your gait. The most foolproof way to do that, is to start going minimalist or barefoot and train yourself to take feedback from your feet.