Lightning has been the most prominent FF character for the better part of a decade now. Even longer counting promotional material. It makes sense that enough people chose her to put her at #2 among 25 characters, even if she's polarizing overall. Kinda like how Obama has been chosen Most Admired Man in America even at his least popular. And before him, George W. Bush.
Admittedly, she also has her good points. Really good design, a powerful female character, and among the least offensive of the FFXIII crew. It's revealing that not a single other FFXIII character made the list.