One of the MCs in my first book is absolutely a good guy. Down to earth and funny, with a strong moral compass and always has his friend's backs. But I think what keeps him from being a Mary Sue is that within the narrative I explained exactly why he's such a sweetheart, based on his background and natural personality. I actually based him on a person I know IRL who's just as wonderful and stand-up as he is. He's not perfect, but he's a really amazing person and there really are people like him out there.
See, I don't think people are shy of making their characters likeable - but I maintain that what makes a character likeable in person is not what makes a character likeable in print. For one thing, you're usually inside a main character's head, with their thoughts and their perception of the world. Barring invasive psychic powers, this is not the case with someone you're hanging out with. You get to hear them say "I love that shirt, you look great in it!", but you don't get the inner monologue that says "I bet she's not even noticed my new shirt, and it cost a fortune too. Let's give her a prod and see," else "Oh god, all I could think to say was I liked her shirt? She must think I'm an idiot!", the same way that you would in a book. If that inner monologue is also going "Oh I love her new shirt," then you end up with a very flat, very dull character who just doesn't grab the reader's attention. There's nothing intrinsically bad about making a character just a really nice person, but it does tend to get stale and predictable if you're not also seeing the side of them that's struggling with something - and not that many people are interested in stale, predictable characters, for the same reason you wouldn't go out and buy a book where everyone just has a nice time and nothing unfortunate happens.
