In the touch-typing method, you hold down a modifier with one hand while pressing the key with the other hand.
The custom started with Shift, and I suppose that that custom just transferred to other keys.
Not all keyboards have two Control keys though. Many keyboards for terminals, Unix systems, Apple II and the very first IBM PC had the Control key to the left of A where most modern keyboards have a Caps Lock key.
Most operating systems allow the Control key to be mapped there and many modern keyboards even do it in hardware. A couple keyboards even come with duplicate keycaps for swapping the legends between left Control and Caps Lock as well.
In most European layouts, the left and right Alt keys are not the same key: the right Alt is "Alt Graph" for making special "graphical" characters. For instance, the characters { [ ] and } are on Alt Gr + 7 through 9.
Oh, and back to the topic: not one but two Windows keys?
If a key is available on a keyboard that they use, that person might start become accustomed to it... I have seen users here complain about keyboards that don't have a right Windows key. (Some have a right Fn and Menu keys instead for some reason)