Antigua Guatemala - Many shops in town sell tickets for the Antigua shuttle, which departs at 6:00AM and at 12PM, pickup from your hostel is all part of the service $20US - February 2012. Journey takes about 6 hours.
El Florido Guatemala Border - A minibus leaves regularly from the bridge near the central square beginning at 6AM L30. From El Florido you can catch a minibus to Chiquimula Q20, a transport hub. Of particular interest in Chiqui is the direct bus to Flores via Rio Hondo, Rio Dulce and Poptun. Leaves from the main bus station in the market at 9:30AM daily Q85, 8 hours. Leave Copán bright and early and you will have plenty of time to get the bus to Flores.