Okay I'm confused. If I spend 17 dollars (ouch) on a ticket from NJ Transit from Trenton, do I then have to pay an additional 5.50 for the air train? I've never flown anywhere where the airport rail cost extra!

I see that Trenton to EWR Train station is $18 to be exact. And you do not pay anything extra for airtrain. The Conductor will return your train ticket after checking and you'll use that ticket to enter into the airtrain from Newark Airport station to go to any of the terminals. Ensure to get down at Newark Airport station (one stop before Newark Penn). Also, night time airtrain schedule is weird, takes too much time and couple of changes.. So make sure to have some extra time if traveling in night

You don't have to pay additional for the air train. You use the same ticket or barcode for the air train

air train is free between terminal rental car etc. $5.50 is to go to and from Penn station. so yes if you com from penn station you will have to pay 5.50