People need to get use to the fact that starting a New exercise program is going to cause some physical pain. The trick is knowing what's reasonable, and what's an injury. I started riding in may. I rode all summer. My knees hurt often. I adjusted my saddle and clears a bit and it helped, but mostly I kept riding. My knees don't hurt at all now.
ifound in my case that my knees hurt on climbs, but if I kept going they stopped. I also focused on keeping my feet aligned with the frame and that made a world of difference.