Our hotel arranged transport there. This seemed to be the easiest way to get there, and allows you to walk down through the ruins and be picked up at the other end. There are two entrances to the ruins. We were dropped off by our shuttle at the Magnesian Gate, which means we were walking down through the site (not that the climb was that steep - but on a hot day...) If not taking a shuttle from your hotel, a minibus ride will drop you off about a 10 minute walk from the lower entrance.
On the way back, we took a dolmus instead of the hotel transport, since we were not sure what time we'd be finished at the site. This worked out well.