Also, he didn’t always make the best impression when he was younger. For example, he has retired from significant matches with reasons deemed not valid by the audience and/or other players. I’m not saying those reasons are valid or not, but it’s debatable, only he knows. And after some years, having the same potential as Nadal and Federer he finally found a way to be able to compete against them and win against them, so I’m guessing he kind of spoiled it for the fans of the other two.
I think pretty much that’s the main reasons. Now, if you ask “is it fair to not be as loved or more than the other two players?”, no it is not, in my opinion. He is at least on the same level overall and just like them his game has unique traits, he has given a lot to tennis, he means a lot for the game, he seems to be a genuinely nice guy off the court too, he is the best at losing, and he belongs in the eternal (and pointless) debate of “who is the greatest ever”. Also all three of them have been douche-bags in some ways in the past, just like everyone else, they are just people after all. The essence (as a rule of thumb at least) is in how we evolve, not in how we used to be.