With the advent of e-ticketing, your ticket will be void with all value forfeited if you miss your train. I believe the Flexible fare option lets you get a refund if you miss the train, but I'm not 100% sure if this is true. This information is from this page. Notice that the wording "If not canceled before the scheduled departure from the origin ("no show"), the entire amount is forfeited and cannot be applied toward future travel." is NOT present under the Flexible option.

If you are flying United, you may want to book your train ticket with your air tickets. That way, if your flight is late, United may protect you by rebooking you onto a later train. The following Amtrak stations can be booked as a United codeshare from EWR:

"Airport" Code - Station Name
ZVE - New Haven, CT
ZTF - Stamford, CT
ZFV - Philadelphia 30th st Station, PA
ZWI - Wilmington, DE

If you're traveling beyond any of these stations you can book a separate ticket from Amtrak on the same train from that station to your destination.