Yeah I never saw it as an issue. It seems... easier to just build a ship in space, but there's no real issue with it being constructed on the ground.
I think a lot of people reacted negatively to it because "The Making of Star Trek" said it was built in space. It may have also been seen as problematic that the Enterprise was struggling in flying in an atmosphere in "Tomorrow is Yesterday." You can easily write this off to the ship's state post time travel. TNG showed Galaxy class ship pieces being built on the Mars surface in "Parallels" but I think that was less of an issue because they were pieces, not the fully finished ship.
I mean, if it's automated and using robots then in space makes sense, or manned pods. But, initially, safer for the workers to be in an atmosphere. I know, I know, humans needing to breath shocked me too...
I'm at least 50% sure that the scene of the Enterprise under water in Star Trek Into Darkness was put there just to stop people complaining about the Enterprise being on the ground in Star Trek (2009). God knows there's no other logical explanation for it...
From The Making of Star Trek, Part II, Chapter 2, page 171: "The unit components were built at the Star Fleet Division of what is still called the San Francisco Navy Yards, and the vessel was assembled in space." So just like the Galaxies on Mars.