AmigaOS 4 does use the MMU, but only to map pages to virtual addresses to for example help with memory fragmentation and swapping to disk.

Here's some surprisingly thorough documentation on this:

http://wiki.amigaos.net/wiki/Exec_Memory_Allocation

However, the MMU is not used for memory protection, not even on Amiga OS 4.

Edit: OK, so not entirely true... See this for more: http://www.os4coding.net/forum/memory-protection-support