It's difficult to know for sure without understanding the context where it was used, but I can think of two meanings:
1) Used literally, it means to travel to and from a destination in the low-cost seating (in the back of the airplane or bus).
2) Used figuratively, it could be used to describe an experience as frustrating or irritating. Example: "I just got off a two-hour phone call with my mother. Talking to her is like a round trip seat in coach!"