The reason you fall sick, say from the flu, is your body being invaded by viruses. These viruses kill your cells, leaving the area unprotected, thus contribute to the aching. To counter these invaders, your body will produce tons of antibodies, which promote the release of the chemical histamine that widens the blood vessels attacked. The wider stream allows more of your defence mechanism, i.e. white blood cells among others, to fight in the infected area. Unfortunately, these histamine might end up in your joints and muscles, triggering receptors to histamine that then causes pain.