No he's not protected.
Croup is usually a virus. BF babies aren't "protected" from anything, they get antibodies for viruses from your milk **if** you have the same virus (Your body is making antibodies to kill off the virus in yourself and you pass them on to LO). That helps them to get over the virus faster than if they were FF--but it can't keep them from getting a virus altogether.
GL with both your boys!!!