The reason why is simply the fact that Luna is an underdog... She was banned to the moon for 1000 years, which is a long time... Also it seems like Celestia is weaker than she was in the past... The memes have also destroyed her... Also Luna is easier to relate to than Celestia because of her past, making her more popular.
Personally I like both princesses, but for different reasons... I probably like Luna more just because I'm such a night person... Also I really love Luna's brash personality and design...
Celestia I think is an actually better ruler though, due to calm and collected nature.