It's the new Navy. In the old Navy, when people screwed up, we dealt with it at the lowest possible level which usually meant an ass-chewing in the Chiefs' Mess and the front office never heard about it. The new Navy lives by the credo "don't be the senior guy with a secret". In other words, nobody is going to put their career on the line and any misconduct is going to go straight to the top.
It's quite possible that misconduct was being dealt with in the "old Navy" way and the Skipper never knew anything about it. But ultimately he's the Skipper, the HMFIC, and it's going to be his ass over the fire when this stuff comes to light --whether he knew about it or not. And if he didn't, he should have, as far as the "new Navy" is concerned.
In the end, Tailhook may have started the downhill slide that killed our military once and for all.