Or maybe people like Sub Zero because they like Sub Zero. Sub Zero and Scorpion were the two main characters, or at the very least, the two most iconic, memorable characters of a video game that had taken the entertainment medium by storm. MK formed the ESRB as a byproduct. So the most popular characters are almost definitely going to be the two ninjas. One is hot, one is cold. One is 'good' one is 'evil'. One belongs to one clan, and the other another. One is Blastoise the other is Charizard. One is Goku the other is Vegeta. One is an apple the other is an orange. One is Coke the other is Pepsi. It doesn't matter what they are in actuality. It doesn't matter if Ed Boon favors one over the other. They are antonym characters which will form a following for many different reasons. To some like yourself, Scoprion is obviously cooler. A fire ninja with a memorable quote and an interesting storyline. A fun gameplay style and iconic moves. For others to prefer the other ninja, to you may seem like an impossibility.
To others, Sub Zero is clearly cooler. He can freeze people, had one of the most iconic and memorable fatalities, has a cool name and comes up in search engines more than the name he's based on. To some, liking Scorpion more is odd, and his prevalence and popularity only further increase one's affinity to a character they've loved. Because of their nature as rivals, it is most likely going to be the same case with fans of either rival, as it isn't uncommon for people to relate to a character on some spectrum. Liu Kang and Kung Lao are on the same side. This is why you have some who prefer one of the other, but there is never a 'rivalry' between Liu Kang fans or Kung Lao fans. Kitana and Mileena are an example of this, but not to the same degree as Sub Zero and Scoprion. No matter what a Scoprion fan says or believes, no matter what a Sub Zero fan says or believes, they are both iconic characters, and have just about as many fans as their adversary. There isn't always necessarily a 'reason' or hidden agenda for a person preferring something. Like what you like, and leave others who like something else alone.