I don't know much about yanderes so I'll leave that aside for now haha.
As for the overprotective main character: I understand the difficulty, because an abusive nature and an overprotective nature share traits like "controlling", "obsessive", etc. I think the key here is intent, and the role of manipulation: an abuser's intent is to manipulate their loved one into staying, into listening to them, into depending and leaning on them, sometimes ONLY them. An overprotective character who's main intent is to protect is different, and what I assume you're aiming for: he's literally protecting his love interest from murderous people haha, and with that comes a hyper-sensitiity, hyper-awareness, paranoia, a HUGE sense of responsibility. His motivation is placed outward, rather than inward: your protagonist is overprotective for the sake of his loved one, while an abusive boyfriend is "overprotective" for his own sake, for the end purpose of using their partner for their own security, confidence, personal gain.
I hope that's helpful! :)