Because a bad video card / drivers combinations can produce all kinds of weird artifacts when hardware mouse support is enabled. Roughly in order of "How much of a pain it is":
* The mouse cursor may not appear at all.
* The mouse cursor may appear, but visual artifacts occur when the mouse is moved (which may or may not have any relationship to where the mouse actually is)
* The mouse cursor may appear, but not change when it should (in response to what lies under the mouse, for example).
* The mouse cursor appears, and changes image correctly, but the "hotspot" (the spot where the application reports the mouse is) and the visual representation of the mouse don't align -- the application and the user disagree on what is being clicked on.
Since the performance gains of using a hardware mouse are pretty small, it makes sense from the developer's point of view to disable hardware mouse support by default just to avoid the potential of problems. Of course, all of the above were issues 5-7 years ago -- I suspect that issues like this are one in a million at this point.
#3 is exactly what is happening to me in linux with the Steam Linux version of the app. The mouse cursor is about 50-60 pixels below where the game thinks I'm clicking... Using an AMD video card.