It's pretty obvious Denethor favored Boromir and would love to take him back and have Faramir gone forever. It's pretty pathetic though that he sent his remaining son to his death because of that.
As far as the 'nazgul flies', he just meant in a straight path. When we say fifty miles as the crow flies, we mean fifty miles straight there. But, alas, roads don't always take us where we straight to where want to go(sometimes quite the opposite
), so it invarialbe takes more than fifty miles to reach our destination. Gandalf was simply stating 'It'll take us three days going straight there, provided no sidetracking or pitstops'.