Yeah, Papyrus is such a perfect little floof ball. He believes so much in you even when you've gone around murdering people. And that's how my shot at genocide was ruined. 
And yeah, I've noticed Sans seems to be really popular, too. For one, I think the more comedic characters always tend to be more popular. But my reasons...
Well, firstly, you can find a lot of depth to him once you go looking for it. I mean, I always liked him, but in the beginning he just seemed superficial next to Papyrus and Undyne. But then, I kept finding these little hints that Sans puts on a front to keep Papyrus (And possibly Frisk and Toriel, in the pacifist ending) happy, and that he's actually seriously depressed. Like, the dialogue during his boss fight shows that he knows about saving and resetting and maybe even about the First Human - not as intimately as you or Flowey, but he knows, and he knows that everything he tries to achieve will likely be undone by it, sooner or later. On one hand, I think it's why he doesn't just immediately come and kill you if you murder Papyrus - he assumes everything will be reset and Papyrus will come back, so what's the point? On the other hand - he doesn't bother improving his situation, and doesn't see any value in trying to, because it will all be reset and he'll be right back where he was. And it lends context to everything about his character - his lazyness, his irreverence in the face of your actions, the hints that knows more and is more than he lets on. A character who first struck me as a shallow prankster archetype suddenly gained a whole lot more depth, and further, it added just another layer to the pacifist ending - because there's Sans' chance to overcome his nihilism and depression and start believing that things can get better and his actions matter.
Secondly - I don't know if you know about Gaster, but he's this huge mystery that was locked away in the game's code. Supposedly he was the Royal Scientist before Alphys, before a lab accident scattered him across time and space. And it's implied he's still alive, still aware, and paying attention - but we know nothing more about him than that. Well, actually, we know that his full name is WD Gaster, and that he speaks in Wingdings font (And that this is the origin of his full name Wing DinG Aster, with Aster being another font family.) which leads a lot of people to speculate he's connected somehow to Sans and Papyrus, and that he may be responsible for all of Sans' strange powers. So, there's also the fact that he's tied into a huge mystery you wouldn't even know about without datamining the game, which attracts people who love to speculate endlessly.
Thirdly - I mean, dude's a badass. He's the weakest boss, but the hardest boss fight because he cheats to hell and back. Dude.
So, I dunno, just a combination of all those things are what really draw me to him. I can understand if it doesn't really do it for a lot of other people, but just the combination of his humor/hidden depths/general badassery made him my favorite.