They are basically the same thing, even run by the same company. Depending on when your cruise arrives in port, the Trolley (on your own) may be the better deal. I'm not sure how some of the cruise lines handle this, but if your ship arrives in the afternoon (Rhapsody arrives at 3 pm), you can take the Trolley tour but they don't let you get off & on. If your ship arrives early in the day, they might let you off and on the Trolley - I'm not sure.
We stayed in Key West a couple years ago and took the Trolley ride. You get a sticker to wear and were allowed to get off the Trolley at the stops and look around at your leisure. When you were finished looking, you could catch the next Trolley - very convenient.
We recommended the Trolley to relatives who were traveling on the Rhapsody. They were disappointed that you couldn't get off the Trolley. Their reasoning behind not letting your off is that they quit running at 5 pm so they have just enough time to make the route before closing. I don't know if you can get off and on if you take the Trolley earlier as an excursion or if you take it that late on your own.
We also took the Conch train in Key west. You don't get off the Conch train. It takes a slightly different route than the Trolley but most of the sights overlap.
Find out whether you can get off and on the Trolley - if so, do that one. If not, they are basically the same tour.