You say he only played Nadal once. Yes in a major, but he's played Nadal 3 times this year. He's won all 3 times, beating him in Indian Wells (where he completely destroyed Nadal) and Miami. Big time events. Plus who of note have Murray and Djokovic beaten this year? Even if Fed had played them, he would have been the favorite against them. And this doesn't include the fact the he beat Wawrinka, the current US Open Champion, on hard in Australia. You can make the case that Cilic was one of the top 2/3 players on grass this season. Cilic and Fed had the two best winning streaks on grass this year and won the two 500 level events.
You can also make the counter argument that Murray got lucky last year to be number 1. Fed was out the last half of the year. Nadal was out a good part of the year and never healthy. Djokovic's game dropped considerably after the French and his head clearly wasn't right. Isn't that luck too?
A player takes advantage of the situation that presents itself. How often in tennis is everyone healthy. You could argue that DelPotro being injured has been lucky for everyone too. One of Fed's biggest strength's is that he's rarely injured.
I think if every one were healthy, based on Fed's level right now, he'd still be the favorite....at least until the momentum changes....as it eventually will. : )