Sadly, I think TWBB got its Cinematography Oscar as a consolation prize since TWBB was nominated for best picture and director but got neither. Same way as Juno got best original screenplay - if TWBB had an original screenplay it prob would have won instead of Juno, but it couldn't compare with NCFOM.
Happily, even though I suspect it won for the wrong reasons, if I was worthy I would certainly have voted for TWBB. From hearing Elswit speak it seems that his and PTA's relationship is painfully beautiful, and as a result transcends what either could do alone. For me that collaboration is the height of cinematography.
Deakins was robbed in 2001 when LOTR beat the man who wasn't there, and without any doubt deserves at least one, if not more oscars. I just feel like Elswit had the slight upper hand this year (although I still don't think that's why he won).