I've had two ACL reconstruction surgeries on my right knee. Took me some time to get a full range of motion back in my knee, but now I use the TRX regularly with no pain.
The TRX is great for exercises that are harder on the knees, such as the squat and lunge. For both of these exercises I would modify after surgery such as changing the Single Leg Squat to a regular wide stance squat with both feet on the ground using the TRX to lean back and keep the weight in the heels. Throw in some sets of holds at the bottom of the squats to really fire those quads. I would start with 3 sets of 30second holds and work up to 5 sets of 45-1 minute holds. Sometimes I thrown in mini reps at the bottom of the hold to challenge myself.
For the lunges, instead of doing the Suspended Lunge, do a regular lunge facing the TRX, but keep your back leg glued to the ground and just slightly bend and straighten the back knee. Again, to fire the legs hold on the bottom of the lunge.
The hamstrings exercises will be key to your knee recovery. I'm no PT, but have been in physical therapy plenty. Don't try to come back faster than you think you should.