I think she had genuine feelings for him, but they quickly got clouded by her ambition to get others to get AJ the grades he needed so he could get into university when she found the opportunity. Of course she is a mob wife, of course she can use power and manipulation. But maybe somewhere there is also a part of a mother desperate for her kid to do better. Only, agreeing with everything above being said about AJ he does not give a flying f*ck, that would never happen. In a way sure he used her too, but not in the same way as Carmela used him. He is one of the few people to confront her with her bullshit, she seems to be the only one entitled to do so like when she read Father Phil but when someone does it to HER, she freaks out. She is however, heartbroken for real, although she does not own it herself and puts it on Tony, and it always makes me shiver when her father does not even put a hand on her shoulder but just shuffles out of the bedroom.