Same can be said for SFO, just replace "thunderstorm" with "fog/low ceiling/too-close-for-comfort parallel runways".

Of all the routes that UA does do some serious padding on, JFK<>SFO is probably the most justified. ORD<>LGA is a close second.

Also, in fairness, if you compare the block times to the actual flight times of routes that aren't as susceptible to weather/ATC delays, they are usually much closer together. DEN-MEM is one that I take just about weekly. I can't recall the flight ever departing or arriving more than +/- 10 minutes from scheduled, with the lone exception being a recent 3+ hour delay due to weather across the top of the country from Chicago to the east coast.