I have said this on these forums before, but maybe before your time, so some will forgive me if I repeat myself.
Roger is a great champion, so he backed himself in both of those matches. As he should have. Remember he broke Novak's win-streak when he beat him in that SF. And he played Rafa pretty well in that final. It might have gone 5.
You say that "Djokovic was a clear favorite" to win the FO that year. No, but you probably mean if he'd made the final. I don't even think that is true. Rafa was basically the favorite every year he played, until the last, I suppose. But here is what people forget about those SFs, and that final, when they make an extravagant comment such as yours: in order for Novak to have made that final, he'd have had to have won that TB on Friday night, which he lost, giving Roger the win, in 4. That TB was played in the last of the light of that day. So, if Novak has won that TB, they'd have had to have come back the next day to finish the match. And, at that time, there was no TB in a 5th set at RG. So that set could have gone easily an hour or more, given how they were playing that match. Meaning that, whoever won that 5th set was going to have to face Nadal the next day with less-than perfect preparation. Nadal had been resting since early on Friday, after a fairly straightforward match with Murray. On top of that, Djokovic didn't beat Nadal the next year when he did meet him in the final, and it took him 4 more years to finally beat Nadal at RG, so it's hard to say he would have in 2011, had he beaten Roger in the SFs.