A lot has been made about the recurring eagle imagery in Hancock. He picks the eagle as a symbol, but never says why. Eagles show up all over in the backgrounds. Some have pointed to this as Hancock being a metaphor for America.
I'm inclined to think that it was a case of Hancock simply not being able to find clothing adorned with a falcon, and the eagle feeling sufficiently right to his amnesiac mind. :)
Y'see, at one point the backstory is brought up that Hancock and the other main super in the story were seen as gods in the ancient past. Well, here we have a guy with "bird of prey" imagery and such a strong commitment to justice that he fights for it even when he can't really figure out why he should care. Yeah, Hancock is Horus. Sky god, war god, god of justice, and one of the few Egyptian gods to survive the syncretic transition into Christianity (as St. Horace). The other gods all died, but Horus lived on to protect the weak.
As for the goddess in the equation, that's a little trickier. On the one hand, Isis was another one to make it into Christianity, both as a saint in her own right and as elements of early Mary cults. Plus, the "cover" name for the goddess in this movie is Mary. But...Isis was the mother of Horus, and Mary was "created" to be Hancock's mate. Sure, some scrambling of myth is possible here, but I'm inclined to think she's not supposed to be Isis, but instead someone who might be considered sister or wife to Horus.
Hathor makes a compelling case on that side. In one version of the myths, she's married to Horus. Her necklace is a circle (Hancock has an eagle pendant), which could be seen as representing Hathor's role as the encircling Milky Way, plus Hathor is often portrayed with a disc atop her head. Among her aspects is motherhood, making the domesticity of her life at the start of the movie fitting. She's also a war goddess in some versions, and one of her later epithets translates as "one who remembers Horus" (more of a pun than a straight translation, apparently, but still). Hathor has syncretized with Astarte as well, as a somewhat nutso war goddess (and Mary's trigger is being called crazy, just as calling Hancock an asshole sets him off).
Anyway...I was pleased that pretty much all of this stuff was deeply backgrounded. Mary never came out and said which gods they were, or mentioned any of her or Hancock's previous names. Just a few symbols and potential mythological resonances. Rather than shoving it in the audiences faces (which, frankly, is neither necessary nor helpful to the main plot), it's left as something for people to figure out if they want to.