So says Science in the Common Interest http://www.soci.org/SCI/groups/foc/20...
"The practice of serving duck pink in the middle is traditional practice in restaurants, and yes there is a potential risk of salmonella. It is suggested that if the duck is not pierced by a knife or similar object then bacteria have not been introduced to the duck breast. This is similar to rare or blue steaks."
They go on to note that it carries the same risk as steaks. By the way, Clusters and Hops carries nice (conveniently packaged) duck breasts for cooking on the grill or sauteeing. Just FYI. (One of my favorite things).
In answer to your question about why it's safe to eat duck medium rare, it's the breast (in French, "magret de canard") that we're talking about. It occurs to me that while chicken and turkey are considered white meat birds, duck breasts fall into the category of red meat and so can be cooked to desired doneness -- I prefer medium rare -- like steaks, lamb, etc.
Squab is another dark meat bird that can safely be prepared medium rare and tastes best that way.