Recently the American Academy of Pediatrics (AAP) issued a press release regarding breastfeeding mothers with possible HN1 infection. There is confusion among the public, and even among practitioners, about the transfer of flu virus through breastmilk. This article could not be more clear: "influenza virus does not pass through breast milk." Many hospitals and practitioners are telling mothers they must be separated from their infants, and even to pump and dump their breastmilk, during a suspected flu infection. The AAP guidelines do NOT recommend separation of the infant and mother, and instead offer a list of precautions to minimize the chance of spreading infection to the infant via contact.
Please see the following article for the specifics:
Advice regarding breastfeeding for mothers with possible H1N1 infection