OS overheads, layers of abstraction for APIs, etc, etc.
There's no mystery or magic. Its just that once upon a time people programmed the hardware more directly, which results in getting more from the hardware.
Computers aren't as simple as they were in the amigas day, so people tend to program for software rather than hardware.
Higher resolutions and color depths, higher quality sound and so on also mean computers are shifting a heck of a lot more data around.
Do this on an Amiga and watch it buckle under the weight.