I think it was partly that you have to be quite well-read in sci-fi to know where the names for the tech, buildings, victory conditions etc. come from, so most people don't get an easy anchor to remember what benefits they're likely to get from their choices.
Probably also didn't help that the first version had a very anti-climactic victory sequence; they improved it, but I do remember it being jarringly sudden the first time I played.
I'm a massive Science Fiction buff and bought the game, played it for a few hours and decided it was not for me. I think it's because I couldn't relate to the factions, if that makes sense.
- Civilization: Beyond Earth