Well if I understand everything correctly you guys started dating when you were 21... Maybe she feels a bit resentment because she never really had a chance to date around or enjoy the single life while in her early twenties. She may also feel a bit turned off as you're a stay at home dad...
I don't know many women who are turned on, while they're out busting their butts and their husbands are taking care of the child and not working...
Now to be fair, since she hasn't complained about the arrangement, then it probably is deeper, but the stay at home dad thing could be a smaller part of the big picture.
As I've said you guys were fairly young when you started dating.
Med school is a lot of work--she may feel stressed out and that you don't really understand her or her job.
Or she may just feel that she's outgrown the relationship. Generally as people age they're expectations, needs, and feelings may change as well. This means that she may have new expectations when it comes to a mate.
It could also be that she's met some male med students that she feels she has more in common with than you.
Honestly the ONLY way I think you can get pass this is through marriage counseling. You also need to ask her why she believes she isn't attracted to you. Is it how you look? The way you act? If she can tell you why she isn't then that will help a lot.
But counseling is a good idea.
At this point I think you guys can still save the marriage--as she hasn't cheated or moved on yet.