I really only think that Monica Reyes fell in love with John Doggett because she felt sorry for him. She must have seen in him that he was in love with Scully and was living in misery because he couldn’t have her. She knew that he would put himself through Hell over and over again over his son’s kidnapping/molestation/murder case - which she (Monica) failed to solve. In both seasons 8 and 9 Monica showed a desire to see Doggett let go of his pain and suffering, and showed viewers that she wanted so desperately for him to let it all go. So I think that her seeing all his pain, misery, unhappiness, and the fact that she is one of the central reasons why he continues to live in grief over his son, and won’t allow himself to love someone available to him - is why Monica Reyes fell in love with him and wants him to love her too. Because if Doggett were to love her back, then she would feel like she succeeded in taking his misery away, and that would make up for her failure to solve his son’s case back in ‘93.
I don’t think that Monica means to have her love for Doggett be for her own selfish reasons, but I think that is exactly what happened.
/rare DRR commentary by Dana Doggett