Of course you realize it's wrong to dislike your SIL and her kids – what you may not have thought about is WHY it's wrong. What if the situation were reversed, and she resented you and your kids because the GPs preferred you? I think you'd see that it is not in your control to make them love you less or the others more. Switch that back to your situation, and you can see the pointlessness of resentment toward her.
As unfair as this situation feels, it really is beyond your control whether or not your in-laws love or don't love people all the same. Do you? None of us do. Are there sensible reasons? No, not usually. There can be a whole host of rationalizations, but usually our likes and dislikes are based on things we don't recognize and can't control. Can I make myself love, or even like, somebody who rubs me the wrong way? Honestly, I do try, and occasionally I can achieve at least a scruple of respect or caring. But that doesn't mean I'd like to hang out with that person.
It's just human. Unfortunately.
Help your son to understand this so he won't be wounded by the lack of care and interest from his GPs. This will be an amazing life skill that he will find useful in many situations. For me, it's Rule #2 for living a sane and happy life: Don't take it personally! (Rule #1: Whatever I hate in other people, I hate in myself, and don't want to face. Rule #3: Recognize that the only things I can change are in myself, not in others.)
I think if I were in your situation, I would try to focus on dealing with my own business, and leave their business to them.
I wish the best for all of you.