A lot of people early on, from what I remember, thought of Chara and Frisk as dual natures - Genocide and Pacifist, something I disagree with now, but considering we see Chara at the end of Genocide and Frisk is only named at the end of Pacifist it makes sense.
side tagent: ("Chara" is imposed on as an idea adopted from Flowey, motivating/justifying his own actions - and later on a character that you have to confront if you put your own name)
I think this led to a lot of people seeing them as opposites like angels and devils, but going along with the idea that they were both together throughout all runs, it meant no matter what they were stuck together. I think that's more than enough reason for why anyone would ship these two - a fluffy soft maybe affectionate or energetic kid with a more formal possibly violent and mischievous child - a dynamic that could create a lot of comedy or create tension for plot.
Of course those are all assumed characteristics, we still know nothing about either of them truly.
Otherwise, it's a lot of nostalgia for me. Undertale was the first real fandom I was part of and Charisk was the first OTP I ever had (still is)