It is very common for a male to become protective of a female puppy. Happens all the time.
Did you happen to catch the info on the puppy's progress that I posted the other day? The First Lady was interviewed by Bill Plante of CBS News, and they played it in two parts just before the inauguration.
She says the puppy has settled in very well, is sleeping in the kitchen of the upstairs residence until she's housebroken. The First Lady says the puppy loves Barney. Beezie is not afraid of anything. She's very bright, alert and playful. She's teething and was chewing on one of Laura's fingers during the interview. The cat does not like the puppy.
All in all, it sounds like things are going great with the pup. Sounds like she has a good temperament, just like Barney does.