I'm staying in downtown Manhattan by myself and figured it might be easier to get to JFK during rush hour via subway. The AirTran site confuses me... how do I do this, how long should it take, and is it safe lugging luggage around?

Terminal 7

Quite correct = getting to JFK during rush hour can be a long trip. The airtrain is very easy. From your lower Manhattan site, get on or transfer to the E train to Queens. Exit Sutphin Boulevard stop ( with lots of other people ) and follow the signs to the Air Train with $5 fare. No changes are required. The airtrain makes a circuit of the airport and stops at all the terminals. Worst case scenario is less than 90 minutes.

I live on 24th and 8th next to the E-train. From door to terminal -- one hour.

Subways can be JAMMED during rush hour (that's how it got its name!), so don't try to carry a lot of luggage. It's not just that people may try to grab what you're trying to carry, it's also that there's not a lot of room to maneuver. New Yorkers do not appreciate people taking more than their "fair" share of room on a subway, so you may find out how they got their reputation for surliness.

while I agree with my colleagues NYTim and Nicolaitan, as you're traveling during rush hour, I would stay off the subway. Instead, I would take the Long Island Rail Road from Penn Station directly to the hub Jamaica. With a minimum of staircase climbing, you can pick up the AirTrain right there. I've taken this route twice, and the AirTrain is quiet and comfy, and only $5 (bring a 5 dollar bill).

footstool is quite correct that the LIRR might be a less crowded and aesthetically more pleasing option, although living on Long Island I can assure you that the trains get pretty crowded too out to Jamaica where many get off and board the south shore trains coming from Brooklyn. A lot has to do with where you are staying in downtown Manhattan since you will still have to subway to Penn Station or pay a fair amount for a taxi.