Fundamental rule of business ...
When you aren't producing desired results and/or are in a position where you feel threatened or challenged by those underneath you, you not only find ways to push those people who threaten or challenge you out but also try to spin it from your position at the top as it being their decision and not yours. You then spend time trying to find "yes men" to surround you such that nobody questions your ability or results.
Jed York is more interested in being the owner and chief decision maker or whatever of the 49ers than he is of being the owner that hires smart people, sits in the background and allows others to do the work, and then enjoys the spoils. He wants both cake and pie. Rarely does that work out well.