To get to the Cyclops you must complete a series of quests.
1. Start the quest "A God Among Men" located on the western side of Kythera Island
2. Complete "A God Among Men" in order to start "Left to Dye."
3. Complete "Left to Dye" in order to start "Stairway to Olympus."
4. "Stairway to Olympus" will lead you to the Cyclops' lair where you can kill him. I recommend staying back and shooting arrows at his eye. Once you stun him go in for melee damage.