Those That Slither in the Dark are obviously the good guys.
Though as for player factions, the easiest way to describe it is that every faction thinks it's the good guys, and that they're doing the right things for the right reasons, but pretty much everyone is wrong about something. So in the end, everybody can wind up as an enemy to everyone else. And most of the conflict could be solved in about 15 minutes if everyone would just sit down and talk about things. But everyone's the hero of their own story - and you really only start seeing the ways in which they're wrong is if you play the other paths as well.
Though it's been pointed out that the color scheme itself can influence the perceptions of people who've played Fire Emblem games for a long time - the Kingdom is blue (the traditional color of the player's units), the Church is green (allied units), the Alliance is yellow (neutral units), and the Empire is red (enemy units). So more experienced players may be influenced into thinking Dmitri's path is the "good" one, the Church is your ally, the Alliance is mostly a distraction, and the Empire is the true enemy.
But as has been said, Edelgard is obviously the real hero of the game. Black Eagles/Crimson Flower best timeline.