I'm 40, I've had two knee surgeries, and have genetically terrible knees. Squatting incorrectly made them hurt, but I went to see a sports PT and he taught me how to squat correctly (I was overloading my quads and not using my posterior chain like...at all - a proper low-bar squat with the glutes engaged was a total gamechanger), and not only did it fix my knee pain in squats, it fixed my knee pain in general. I went from being functionally crippled in my 20s to competing as an amateur powerlifter and training Brazilian jiujitsu in my late 30s, and I absolutely attribute the foundation of that to squatting and deadlifting.
In my personal experience, as a now more seasoned lifter, most people have knee pain in squats because they load the quads and arrest the squat early with the quads rather than hitting full depth. Once your hip crease is below the top of your kneecap, your quads are no longer bearing the load! If you're stopping the lift prior to that, then you're applying a ton of torque to the knee directly with the quad, rather than letting the much more robust posterior chain absorb the energy of the descent.
If you haven't tried squatting low-bar, you might give it a go - it makes it much easier to move with the posterior chain. https://www.youtube.com/watch?v=bs_Ej32IYgo is my single favorite squat video on the internet. Lots of really good info in it.
But, if you don't see improvement, I highly recommend seeing someone who can diagnose and correct how you move.