Prior success is not a perfect predictor of future success; we end up with a positive bias that things are not that bad given the previous outcomes, and so risk rises over time. Overall, I cannot fault a Captain for rejecting a clearance where his judgement on the spot is the final legal authority. The controller, dealing with the issue also seemed to manage the disruption in a reasonable way from his perspective, however the questioning of the Captains judgement tends to look bad in the subsequent enquiry when the wheels thereafter happen to come off the wagon. NY particularly JFK's airspace is a mess, and the controllers are dealing with lousy layouts and options, which the radar guided holds suggest was constrained by the available controller options.
Overall, the guys seemed to keep their cool and the end comments were professional, it was appropriate for the captain to make comment, and it is also appropriate for the controller to explain the issues related to the airspace that he has to work within.
Years ago, a foreign wide body going into a notoriously irritating airport was given the weather which was favoring the long runway, and asked for the long runway, even though flow control was using a shorter runway with gusty xwinds, and being wet. The controller went to great pains to talk the visiting widebody to accept an at best marginal runway, when a very good option was obvious. After 5 minutes of haggling, the controller got his wish, and the visiting aircraft relented and accepted the lousy option. I piped up and commented that it would look pretty stupid in an enquiry if that plane ended up with dirt onits treads from some event on that runway, having been hounded to making a decision that the captain and crew were obviously not happy with. About 5 seconds later, the controller changed the runway for the arriving aircraft and they landed on the best choice runway.
We are a system; the controllers and the flight crew are in the majority professional at their duties and will bend over backwards to do things efficiently and safely, not in that order. Sometimes, the wood gets lost in the trees, and it is worthwhile appreciating the other components that are needed to make the system work.
In the end, the PIC has the legal final responsibility in respect to the disposition of his/her aircraft, and thats unlikely to change anytime soon.
Given how bad the design of JFK is, and the amount of lousy weather, it is a wonder that so few issues arise to the point of commentary.