help me please i'm depressed about this fitness injury?

I have a quick question regarding injuries. I've been rehabbing a knee injury for a few weeks now (runner's knee...if anyone knows what that is). I've been doing uphill walking per the permission of my physical therapist instead. Overall, my knees have gotten better, but here and there I have days where they seem to hurt more than they did the day before, despite the fact that I haven't missed doing my strengthening exercises, icing, etc. Is this normal, to have days where they DON'T seem to get better?

It's just that everytime I have a day where it hurts slightly more than the previous day, I feel like I'm never going to be able to run again. Am I being irrational here?