Is little muscle pain after cycling considered to be a sign of insufficient protein in the body?

No.: Geeting adequate nutritional support from increasing protein is good, but you are experiencing delayed soreness of exercise, which is common. One possibility is that your seat height adjustment is off. Aleve (naproxen) or Motrin should get rid of pain. If the pain is present longer than 2-3 days, you may have strained/sprained something, but you did not say where you hurt! see your pcx if pain persists!