Actually, Nadal really took it to Federer even on Fed's best surface (grass). And I believe the record on hard court is something like 2-2.
Nadal's being a leftie is a problem for Fed's backhand but if you watched the game, Fed was most troubled on the forehand side. He actually dealt with his backhand shots quite well. I understand that Nadal is an excellent player..but I'm a huge Federer fan and I watch virtually each of his matches and things that he excels against other opponents he suddenly can't do against Nadal--and I'm talking about things such as unforced errors that he would normally not make, low first serve percentage, total lack of aggressiveness (not coming to the net...not varying his backhand with some slices, which he normally always odes), and languid body language.
Best example of this would be that five-setter final on clay last year (Monte Carlo or Rome) where I believe Federer had match points in the fifth and then collapsed and had the match stolen...or the French open final last year where he came out firing in the first set and then his level of play suddenly dropped exponentially...
Even on those other surfaces, it can't be said that Fed dominates Nadal like he dominates everyone else.