Delays are never pleasant and any carrier can experience them, air, train, ship. Another thing can cause delays: traffic!
These delays can and do occur all the time by every means of travel because there are simply too many variables that can affect the timing of a trip, i.e., the time it should take vs. the time it "might" take. Keeping in touch with your carrier is one, although maybe limited way of managing time delays in travel.
There are also many Apps that can assist travelers with devices capable of utilizing these Apps to help experience efficient travel (or inefficient) because there is more information readily available with which to ascertain status of transportation methods with great accuracy. Here is a compilation of many travel Apps rated by some of the best sources in the world:
Yes, Amtrak has delays and in NYC, there is usually a valid (albeit frustrating) reason for the delays but the service is usually very good; it's constantly improving and used all around the country. The company has been around for a long time. Experiencing delays in NYC can't be unexpected; this city is big and complicated and it is also no longer the same city it once ways. In many ways, it is better than ever, on another level, things are indeed somewhat inconvenient but generally safety related. The size and volume of traffic (all means) coming and going into and out of NYC is staggering, though more often than not, it works well. I've used mostly all of the various major train services we have.
As for arriving by air, weather conditions optimal, it is a virtual certainty that when arriving into Newark Liberty Airport (an "NYC" airport that is in northern NJ and offering easy access to NYC) and so I never, ever use it. On one level, another airport is more convenient to me and on another level, well, circling in the sky annoys me, and concerns me. Why is Newark plagued with delays? More travelers, not enough runways. There may well be a window of time whereby landing in Newark incurs fewer delays, but if there is, I don't know it.
I've been through frightful delays on BritRail and TrenItalia but that doesn't mean I won't use them again. I've learned from those trips and how delays might have been avoided and second, there are no other trains running in those countries! Amtrak is pretty much IT in the USA and I only wish we could get the rates that visitors get, but then we get rates overseas that locals don't get so it evens out I suppose!
Delays just bite - and carriers know that too, generally wishing to provide great service. there's no doubt about it but technology, experience and preparedness can help any traveler because delays happen. Hence I bring reading material, music, technology, call ahead, etc. But will I be delayed again? Yes.
As for car traffic and all those wonderful weekend getaways people take? If you live in NYC, for most of us, traffic (that's just getting out of city limits) is so prohibitive many of us opt not to travel on those weekends. Do we suffer? Not necessarily because whoever DOES leave, makes the city that much more pleasant and less crowded for us to enjoy our city!! Helicopters are an option for some - but not most of us...and a private jet - well that same traffic would inhibit getting to the airports!
Folks living in more suburban areas not used to big city delays might definitely feel more disappointed by the delay and I completely get that.....makes me wish I lived anywhere there weren't 9 million people all around me, in a hurry, all the time!!
Transit systems work - don't give up! There's an App for that
However, if you ever want to experience almost perfect train travel, take a ride in Switzerland and Germany - absolutely on time in a way that seems impossible...so if you are looking to make a train that indicates a two or three (average time; it will be specific per station) minute station stops - don't think you'll have an extra 30 seconds to make it. You won't. AMAZING.