I've had knee problems for many years and the one thing that every Physical Therapist i've seen has said is ICE.
If your knee is hurting Ice it as soon as you can. Ice for 15 minutes repeat hourly as necessary.
I probably break out the ice pack every other week or so, but I do so at the first twinge of knee pain...nip it in the bud or something.
I found that a day of rest between commutes was extremely beneficial when i was starting.