Good question JSrombough since I was unaware of any transit systems that ban luggage.
Just an OMNI Point of reference: if you take the bus from EWR to Penn Station, NJ... The Airlink Bus allowed luggage (of course) but be warned the drivers of any OTHER bus that goes to PENN get very angry if you try to go on with luggage.
The drivers scream "put your bags out of th aisle and under the seats." One driver turned off the bus engine and said she would sit there until all the bags were either under the seats or the people off the bus.
I take my bags on the PATH all the time and sometimes the passengers get very testy even with enough room for them.