There are a few common causes of breast pain (letdown reflex, producing too much milk, thrush, engorgement, mastitis). You can refer to this article to identify the cause of your and see how to go about relieving the pain:
http://www.babycentre.co.uk/a8489/breast-pain
As for flu, you can continue breastfeeding. It is beneficial for the baby as you can pass on the antibodies specific to your illness and help prevent the baby from getting it (or at least help the baby fight the virus if he/she has been infected).