The obvious reason is that the speed of the transfer varies over time, and so does the average, and so does prediction. To explain this to a non-tech friend, I've used an analogy involving travel by air. You're going to fly over the Atlantic. When you arrive with a taxi at the departing airport, your ETA is about two months. When you disembark at the arriving airport, based on your average speed so far, you will reach your friend's house in 5 seconds.
But you need to appreciate how much the speed can actually vary, even with what seems like a predictable scenario, like copying files within the same disk, or between two local disks. One of the new features I like in Windows 8 is the ability to graph the speed over time if you click "more details". If you don't have access to a Windows 8 machine, search images for Windows 8 copy dialog for a lot of examples. Many of them are fairly flat, but many of them are also disturbingly bumpy, to the point that you wonder whether the hard drive is actually healthy, when it dips to zero.
Some of these bumps are likely due to variations in file size—smaller fields yield more accesses, which slows things down, especially on a mechanical hard drive which has to seek by moving its read head—but some it might just be a cheap drive which stalls on the slightest touch to prevent damage to the platters.
There are better and worse ETA prediction algorithms, but for an accurate prediction, the computer would have to be all-knowing. The risk of trying to make the algorithm "smart" is that it might create new, unforeseen, cases where it's even more hilariously wrong.