I know I'm a little obsessed with the San Francisco Giants, but they're just such a good example of how not to run a professional sports organization or any business, for that matter. And Bill Neukom's departure is a weird story as far as I'm concerned. The article speculates a lot about financial issues (ie - spending too much on a crappy team), but if that's the core of the dispute, then the Giants are even dumber than I thought.
Financial success is directly related to success on the field; over the last seven years, the Giants are last in the major leagues in runs scored. Some of that is the offense-suppressing nature of their home park, but a lot of it is just poor roster construction. Teams simply cannot win if they have no offense, and it has long been obvious that Giants GM Brian Sabean has no idea how to build an offense.
So we essentially have two possibilities:
1) Giants ownership actually thought they had a good team and that the off-season expenditures on players like Aubrey Huff were justified. The implication is that ownership also thought Sabean was a competent GM and that they had no idea how much luck was involved in winning a World Series.
2) Giants ownership is focused (correctly, IMHO) on process, gave Sabean (and Neukom) a bit of latitude because it would have been tough to cut costs following 2010's apparent success and is now pushing for better management. Given that Sabean's contract was extended under the previous ownership group, it is entirely possible that this organization is now actually aware of how incompetent he is.
#2 would be a great outcome for Giants fans, but it's hard to believe there isn't still some irrational attachment to the general manager who was at the helm of the 2010 World Champions.