Pt is really a personal thing---in many countries of the world---like the UK--most folks do not have formal PT and their knees turrn out just fine. But in this country we are obsessed with "getting it right" and making sure we are the best at recovering, so most of us go to PT.
If you were an 80 year old lady who just wanted to play with her grandchildren without pain---PT would seems a little silly. I, on the other hand, am a ski instructor and wanted to make sure I could ski again. I did PT for 3 months---and loved it.
I think your PT's remark that your hamstring is scared is a little childish as an explanation--my PT used a skeleton to show me the exact site of the muscles and tendons as he referred to them. After surgery, our muscles are weaker---is it not unusual since they have been exposed to the air and moved around by the surgeon. My own quad took some time to "wake up" and get back to work. I could not train the muscle until it was firing.
If your muscle is not firing (contracting) when you want it to do so, you can use E-Stym which used a mild electrical current to force the muscle to contract--and thus wakes it up. or you can gently stretch a muscle which is not firing and has possibly contracted a little.
Of course all of this is affected by swelling. Think of a garden hose filled with water---you cannot bend it right? If your knee is filled with liquid, it is not going to bend either. As the swelling is assimilated back into your body, it will be easier to move your joint.
I had adhesions in my left knee and eventually had to have them removed. My OS was adamant that I was not to do any pt for 3 weeks. and then, I started very slowly rehabbing the knee. I did not strengthen the knee until 8 weeks. The OS felt very strongly that adhesions are formed when we do overly vigorous exercise on a hot, swollen knee. My PT was fanatical about making sure all of the swelling was gone before I began to strengthen the knee while weight bearing. the end result? my rom is145/0.
I will add that it took me almost two months to get to zero on the extension---I would gently let the leg hang over the end of the bed every night for about 5 minutes or so.