The ACL is so important for controlling the shear forces at the knee, stabilizing the knee. When it poops out the hamstrings have a huge role to play taking over the shear/stability job as much as they can.
Is it possible that your quad/hammie force is out of balance for you on the bike?
Keep doing all your hammie exercises, so that at the very least they will help your knee by virtue of sheer bulk; but also ask your PT to check you on the bike and help you adjust things so you kick in the hammies more if that is needed. (and this is something a PT should do, since a bike shop will be aiming for a different standard which isn't going to be the same as needed for a stretched or torn ACL)
You might want to take a peek at "Andy Pruitt's Complete Medical Guide for Cyclists" Velopress 2006.
"If Americans want to live the American Dream, they should go to Denmark." - Richard Wilkinson