don't blame the video card manufacturer if you mount your motherboard upside down.

if you really want it the other way get a case that mounts the motherboard on the opposite side of the case.
there are a few around.

I would guess it's more for compatibility purposes, not all motherboards have free space above the PCI-E slot, while it's pretty much guaranteed that there is room under the card since the PCI-slots are there.

Simple... So it wont absorb the heat dissipated by chipset or the processor. ^_^

Generally there are no heat generating parts below unlike above.

This actually goes all the way back to when motherboards were originally layed out and designed. I doubt that Steve Wozniak or the engineers at IBM gave any thought to how gpu's and other add in cards were or were not going to be oriented. Before the desktop computer, motherboards were mainly used in mainframes and servers and arranged in a horizontal drawer like arrangement, the conecpt of the "blade" server wasn't even imagined. Heck it wasn't until the mid 1980's that add in cards started to catch on, let alone be standard operating practice. Truth is, mobos were originally layed flat on the desktop (IBM design and the AT form factor) and it wasn't until Intel introduced the ATX form factor in 1995 that mobos started to be mounted vertically rather than being layed flat. But by then, the industry had become so accustomed to the original mobo layout popularized by IBM that they just "improved" on the existing design. Intel attempted to change the overall layout of the mobo by introducing the BTX form factor which re-arranged components on the mobo to move the heat producing components and provide a better "straight-through" airflow. The BTX design also incorporated "inverted" expansion slots which would have put the gpu heatsink and fan on the top rather than underneath towards the bottom of the case, ala ATX.

because of the cpu heatsink... that simple

Chunkymonster is partially correct. He is only thinking of ISA cards. He has not considered MicroChannel Architecture which the PS/2 carried. Specifically the model 60's and model 80's carried the mobo vertically to make room for many additional cards, primarily network cards (token ring), memory cards to allow for 16Mb of memory (my personal PS/2 80 ran 64Mb of memory when the published limit was 16Mb by using a modified memory manager out of Austin. The primary reason MCA died was IBM tried to license it to vendors whereas ISA was free and the cost of making such a mother board license costs aside was much more than an ISA board. Quantity won out over quality. Like the majority of the PC world with the exception of a few industrial strength servers PC's are the lowest common denominator. Cost is the overriding concern, quality and capability is last in such considerations.