Yeah a lot of the weighting on this award is run by mob mentality. That Golden Ball got Messi more criticism for his WC than Ronaldo had for his (lol) so it's naive to count that as a positive factor for Messi. On the other hand, Ronaldo possesses the only two things the public ever notices: goals and trophies. Those are the only factors that ever come up in the discussion or debate about Ballon D'or. Even if by some chance Messi can rack up some 15-18 or so assists in the remaining 12 games, people will still only notice Ronaldo's scoring rate. What's an even bigger possible downside is that if Messi doesn't perform in El Clasico (i.e does worse than Ronaldo and/or Neymar/Suarez) then he'll get shit on further, to the point where media will say he wasn't even 2nd best. It really does all seem to be in Ronaldo's favor at this point. It'd take something on a 2012 Messi-esque level of miraculous to change that. Maybe the UCL/La liga all time records? I dunno.
That isn't to say that Messi deserved it anyway. Though on a game by game basis Messi's overall impact is far greater and more vital than Ronaldo, he didn't do anything this year to catch the public's eye other than the hat trick in the Bernabeu and the group stages of the WC.