The pain is caused by the "stretching" of muscles and tendons affected by the surgery. During course of physical therapy you will have decreased pain as tendons and muscles strengthen.
The pain is there to let our body know it has reached it's limit. You are recovering from a traumatic injury, not a minor scratch. Feeling pain is normal.
First and foremost, a surgery has just been finished and internal wounds are still healing. Pain after acl surgery could be signs that there is a blood clot.