I keep worrying about the underwater part, too, but the Spore trailer clearly shows the underwater guy swimming around. It doesn't mention anything about underwater civs, but at least it's got some parts devoted to it.
The crazy thing about an underwater civ is that, if it's already in the game, then the physics to handle flying would be in there, too. So, it wouldn't be much of a stretch to have flying animals in the game--they'd still need to be anchored to the ground for their buildings, just like land / underwater. Even if they just fly in the sense that they're off the ground when they move, though it may be by only a few "feet", this would be a cool little feature.
Whatever, if you're a land-based creature, it would be cool to navigate your UFO down into the water and watch the environment kind of swallow you up (ocean-wise) as you went in search of things.