bike...good! pain...bad! Are you "mashing" your pedals (riding with a lot of resistance) a lot? I think that we beginners tend to do that, and it's good to work on keeping the bike in an easier gear and moving those legs faster. Also, find a really good "go to" woman or man. I had nagging hip pain all summer, the VERY nice man at the LBS had set my seat about 1 1/2 inches too low - this after eyeballing me sitting on the bike while he held the handlebars. When I talked to a cycling coach, I said, "pain here." He said, "seat too low." Ya gotta find the people who know, as opposed to the people who think they know....

Let that knee get better! Cold compresses, arnica, rest - can you take a break from the exercise that stresses the knee and do other things - swimming, yoga, weights?