I think the idea here, is to provide guidance for further study by Kepler, narrowing the search space.
I mean, the 'Habitable Zone' for moons orbiting a hot Jupiter, would be completely different from the 'Habitable Zone' for a planet orbiting a star, which would be different from the 'Habitable Zone' for a planet (somehow) orbiting the centre of mass of a binary system, also (??).
Just because Kepler can't detect exo-moons, doesn't imply that there's no habitable zones at smaller scales .. and the same goes all the way down the scale ladder (as Carl points out in the case of right here, on Earth).
At the end of the day, I think they're only trying to provide theoretical guidance to the exo-planet hunters, within their detection capabilities.
Aside from water, oxygen in the atmosphere would also seem to be important, although I read the other day about some bacteria which metabolises sulphur .. which could be present where there is no water, or oxygen … the diversity is almost limitless .. and this latter point seems to be consistently reinforced with more solar system and exo-solar system planetary/moon research
Cheers