That article says the opposite of what you claimed. That is, they acknowledge that some people made the accusations, but they explicitly state they found no evidence:
The game's sheer success has led some critics to accuse Nguyen of using shady practices — including buying traffic or paying for fake reviews — in order to help Flappy Bird ascend the app charts. After looking at the data that corresponds to when Flappy Bird started to build word-of-mouth buzz, however, we can't find any signs of impropriety, or manipulation of reviews or ratings.
The game's sheer success has led some critics to accuse Nguyen of using shady practices — including buying traffic or paying for fake reviews — in order to help Flappy Bird ascend the app charts. After looking at the data that corresponds to when Flappy Bird started to build word-of-mouth buzz, however, we can't find any signs of impropriety, or manipulation of reviews or ratings.