^Also, the writers were very clearly placing Hera in parallel with Starbuck. Hera drew the stars. Starbuck remembered the song. Both are separated from their parents by different means. In addition, Boomer shared a projection with Tyrol, a Cylon. Hybrids navigate the basestars. Hybrids are see things and feel things that others cannot, just like Hera and Starbuck. The implication is that both Hera and Starbuck are also hybrids, which makes perfect sense.
Hera's parents are Helo (human) and Athena (Cylon). By process of deduction, we know that no member of the final Five can be Starbuck's father. We know her mother is human. So, we're left with the 8 models. Unless one of the existing males (Cavil, Leoben, Doral, Simon) is her father, we're left with Daniel, one (or more) of which somehow survived Cavil's actions.