These rankings are based only on domestic league it seems, judging from the number of goals. (let me know if I'm mistaken) So that alone weakens this ranking as a source for the best player of this season.
With that said, Cristiano was not performing to his best at the beginning of the season. He was not scoring as much as he used to also. Zidane also has chosen to not play him against lower tier opposition this end of the season, which could have likely boosted up some of his stats and overall ranking.
Let's say it included all the other competitions. Even then it wouldn't work for me because this rating system treats every match as if all of them had the same value. Should a game against Sunderland or Sporting have the same influence on the overall rating as matches in Champions League quarterfinals, semis, final? I don't think it should be this way as it's easier to get a good rating against the teams I mentioned than to do so at Champions League crucial stages.
The reason Cristiano is in pole position to win the Ballon D'or this season is because he has been crucial at key moments this end of the season for Real Madrid. I see players above Cristiano who have been nowhere to be found when their team needed them to perform in crucial matches.