When Starbuck had to leave him behind on Caprica, she gave him her dogtags as a symbol of her promise to return. For a long time, it seemed President Roslin wasn't going to allow her to keep that promise. Starbuck's obsession with Sam Anders prevented her from moving forward with Lee and also inspired her to behave in battle with a greater degree of self-preservation. Finally, she was given authorization to rescue him from Caprica, and before long, the two of them settled on New Caprica together.
After her single night of passion with Lee, Kara proposed to Sam, apparently recognizing that it was the safe, smart choice. Unfortunately, her married life was interrupted when the Cylons occupied New Caprica, due to Cylon Number Two, Leoben, taking her prisoner and forcing her to live as if married to him. By the time New Caprica was liberated by Galactica, Kara's psyche was too scarred to return to her relationship comfortably, and she began dancing between Sam and Lee, keeping both at arm's length.
Since her "death" and return to the fleet, Kara has made it clear to Sam that she would kill him in an instant if she learned he was a Cylon. He has understandably therefore declined to tell her that he is one...meanwhile, they occasionally frak, and he clearly hopes with all his heart that she will turn out to be a Cylon too.
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