The only fare control station's on the entire AirTrain are the one's at Jamaica, and Howard Beach. All other's are uncontrolled (free). If you wanted to save the fare from the airport to the subway, you could ride to the Lefferts Blvd. stop, and do the walk over to the Howard Beach station. I haven't done that, and it may require a "roundabout" route, due to barrier's that are there to discourage just that. Another way to save, would be to take the Q10 or Q3 local bus routes to reach the subway at either Kew Gardens or Jamaica, and with a Metrocard only pay a single local fare ($2.75).
One thing the AirTrain does, is discourage 'local' rider's looking for a quick way to get from Howard Beach to Jamaica...if you took the AirTrain, with a transfer at Federal Circle, you would have to pay $10. for that ride, paying to enter, and to exit.
BTW, if anyone at the airport wants to just 'waste some time' with a joyride while waiting for your flight, you can ride from the airport the entire system free, as long as you don't get out at Jamaica or Howard Beach, and just go back.