I disabled mine because it was causing the window seal to wear out on the passenger side of the car like here:
http://www.ft86club.com/forums/showthread.php?t=11682
If you don't keep your car clean it could cause issues with window scratches or tint scratches:
http://www.ft86club.com/forums/showthread.php?t=55995 <-- this sucks because you have to fix it immediately or not use the car, because even if you don't use the windows, you still make the problem worse just by getting in and out of the car.
others want to keep the window from rolling up/down while waiting for window tint to set up, or window freezing up do to snow/ice.
As someone who keeps vehicles for extended periods of time (more than 10 years average) I just personally think that it will over use and cause premature failure of window motors/window tracks, combined with window seal wear, glass scratches, tint pealing/wear, I see no good reason for the windows to do this in the first place. The windows do not contact the body (on my car) when completely up and opening/closing the door, and it properly seats into the pocket of the window seal. The only reason for this "feature" that I can find, is to alleviate cabin pressurization when closing the doors, so you don't have to slam the door to get it to latch.(which I don't have to anyway with the windows up) (*note that your door and glass are adjustable, and they could be aligned higher than mine, so if you do disable the window indexing, check to make sure yours do not hit before shutting the door)... (my passenger side is much closer than my drivers side)