IMO it was not fair. Messi didn't played well in his present club compared to the performance of Ronaldo in at El Nasir. I believe he actually won the Ballon d'Or because of the world cup he won and he had performed and manage his countries team to win.
Earlier today I had some conversations about this and led to some argument with my freind and neighbor. Most of them were sentimental because they love Messi and a loyal fan to him. One of them said something that changed my mindset. He said in other to win the Ballon d'Or it does not depend on the voting strength its different now. What is important is your input to the team you play with. When Mudrich won the Ballon d'Or he won world cup and played very well and his impact to his team was top notch.
Just win a world cup and you win the Ballon d'Or