You picked Batman as an example? The guy whose parents died, then he uses the vast wealth to learn and buy gadgets no one else can afford to fight crime. He constantly gets beaten right off the bat (pardon the pun) and his whole arc is to use his intellect to learn from his mistakes to do better after he fails and people get hurt. He is liked because in a world where everyone has some weird super power he is just a guy dedicated to making sure children don’t have their parents killed, too. He has a moral compass and a vision and we constantly see him fall down and get back up. A lot of the issues people had with Superman (an actual Gary Stu) were rectified with Batman. Debates on his vigilantism have made him both a loved and hated character. The question is constantly asked if he might be doing more harm than good. He has doubts and questions himself, he makes mistakes, he isn’t universally loved, he is no where near a Gary or Mary Sue.