Over the years I've found my homebrew 6502 computer to be an incredibly valuable way to experiment with and understand computer hardware concepts. I've learned about clock signals, memory, buses, address decoding, and memory banking; I've built my own video and audio output circuits, and keyboards that connect straight to the bus; I've experimented with the 6522 VIA's timers and shift register, and wired peripherals up to that. I've also learned a lot about digital electronics, how and why things work, and what not to do!
A lot of what I've done has been driven by understanding how the BBC Micro that I used in the 80s worked - but I'm also interested in other concepts that were less relevant on early 80s microcomputers.
Protected memory systems had existed long before the 6502 was produced, but were only relevant on much larger systems, which had multiple concurrent users and enforcing privacy was important. In later decades, running partially-trusted software became so important that computer security became relevant for home users as well - but for the general applications of a 6502, especially with the memory constraints of the age, it was never very relevant.
Nevertheless, even if these concepts aren't useful on small 8-bit computers, they're still interesting and educational to experiment with. The simple architecture and lack of advanced features built in to the 6502 itself mean that you have to create the more complex systems yourself - and this means you have the freedom to try doing it in ways that make sense to you, and discover the pros and cons yourself, without being forced to do it in the way a more advanced CPU requires you to.
I don't particularly expect to make a useful protected memory environment on my 6502; but I do hope to make something simple, elegant, and understandable, and learn a lot in the process!