The initial difference seems to be in how people view the controls. It's really about mentally mapping "push forward" = "tilt the view forward" vs. "push up" = "look up". Consider a coordinate system where the x-axis represents left/right, the y-axis is forward/backward, and the z-axis is up/down (so your monitor is [most likely] in the +y direction, and the ceiling is in the +z direction).
My mental mapping suggests the mouse moves on the xy plane, so pushing the mouse forward represents pushing it away from me and into the game world. The alternate mental mapping seems to suggest the mouse is "actually" moving on the xz plane, so pushing the mouse forward represents sliding it vertically up the monitor.
Of note: the first time I saw the option "invert mouse y-axis" where it meant "invert checked" = "forward is tilt forward" I was confused. Before that, the option meant "invert checked" = "up is to look up". So the term "inverted" is already a loaded question.
Other than your entry into 3D interfaces and how you initially map the controls, I imagine most of the preference is what you're accustomed to. Because I've been playing with the "forward" mentality for a very long time, I'm accustomed to it and prefer it. It's ingrained enough that I quit playing Eve Online about 10 minutes into the demo when I discovered there was no way to invert the camera control from the default "up" mentality while in space.
(For the record, I think Eve actually uses a "grab" mentality, where you're supposed to imagine you're grabbing the front of your spaceship, then spinning it the direction the mouse moves. The problem is that the entire game world spins with it, so my brain automatically reverts to the FPS-style control mentality.)