For the same reasons we have closed source software in almost every device we use now a days. These reasons have been discussed all over the internet since people became aware of the problem. You have heard of Richard Stallman right?
Mostly it boils down to the fact that those that make things to sell don't generally want to tell you how they made it or how it works for fear that you will not buy it if you can make your own or someone else will eat their business. This has been the case for hundreds if not thousand of years. See the story of Venetian glass makers on the Island of Murano: https://en.wikipedia.org/wiki/Venetian_glass
A couple of thoughts:
1) Before worrying about the closed nature of the Pi how about worrying about the closed software in everything else you use: Your PC BIOS, the software in your PC system management chip, in the PC GPU, in the controllers of disks, SDs, USB devices of all kinds, routers, TVs....
2) Why are you singling out the Pi? The way you phrase the question hints that there are other platforms that are totally open. Are there such things?
3) Students can study how software works down to whatever depth they like using a Pi. They can even go further and study how things work below the software, you can run hardware design tools on the Pi. True they can't get into some corners of the Pi itself.