The winner writes the history books, that's why I think in my personal opinion. Since Septim was Emperor, he is known for uniting all of Tamriel and bringing peace to the province. Not for the rather ugly things he did also.
And many people have brought the idea of the Dragonborn ascending to godhood or something along the lines when he/she dies. I'm pretty sure our characters have done quite a few dirty things since there time in Skyrim began.