I don't understand why people get frustrated at schedule padding -- you don't give your ETA from the time you get on the highway to your first exit, but from door-to-door. This is nothing different. JFK and the airspace in the NE is always crowded, there's always a long line for departure, it's nothing new.
If Delta didn't think they would use that hour-and-change sitting at JFK or at MSY, they wouldn't schedule it. This way, you can know what to expect. It'll probably even be right.