I was thinking the same thing at first. But then, isn't the "bio" short for Biology? A biodome isn't underwater either, it's just a contained biological environment.
"Bio-" is a prefix meaning "life."
I just think Bioshock brand-title is now pretty much so synonymous w/ Rapture and the underworld dystopia after TWO games called this, calling this new game in the sky "Bioshock" to me just seems very odd.
I could be wrong - but it just seems like from the way the designers are talking so far, Infinite will also have nothing to do w/ the story of the other games or lead into the birth of Rapture, either.