It was a bad call from Federer, to make comments like that. I'm sure he didn't like Novak, partly because of his retirements and partly because he saw that Nole was not afraid of him, or in awe of him like most players on the tour. But it's true that Novak has earned Roger's respect with time.
I appreciated Roger's comments to Novak after the WTF final very much. He said: "Congratulations, Novak, you're the best...I can't play much better than I did today".
That's amazingly gracious after such a painful defeat, and I know I'm not the only Nole fan who has a new-found respect for Roger after he said those words.
If you people are referring to that remarks in 2006, it was a Davis cup match for gods sake. Special circumstances and lots of things are being said during dc tie. I am sure fed was just reacting to and helping Wawrinka, who was clearly distraught by Djokovices behaviour in that match. Bad comments, but in the heat of the moment, augmented by the davis cup team atmosphere...
What happened next wasn't nice. Djokovic' parents got involved unnecessarily and started harrasing Fed not just via media, but also during matches.. Can you imagine Nadal's or Federer's parents stoop so low as to shout at their sons rival from the stands and make calls? Then public statements like "king is dead", or "my son will never lose to him anymore"...
This made the relationship much worse, and had to be cleared over the longer period of time.