Two rough rules of thumb I use when getting a bike fitted:

Pain behind your kneecap= seat too low

Pain in the back of your knee= seat too high.

Paying a pro to set up your bike can really help. Minor adjustments can make a huge difference. I think a lot of fixed riders are unnecessarily resigned to their knee pain. Fiddling with fit solves a lot of problems, you just have to keep trying things out. I figure if 55 year old randonneurs can do PBP and not have the lower half of their legs fall off, there's no reason why a young person whos just commuting and dicking around shouldn't be able to be completely comfortable on their bike, fixed gear or not.