Adding to this historical reasoning, it is to be noted that in traditional Unix, /usr was pretty much the equivalent of /home in Linux systems: the parent directory for user home directories, i.e. 'usr'.

The existence of /usr/bin can probably be explained by the reasoning that, just like nowadays Linux systems often have a really big /home partition, early Unix systems eventually ran out of space for whatever volume would hold /bin, and with 'reinstalling' not remotely as easy an option as it would be these days, storing an extra 'bin' etc. directory in the 'larger partition for user directories' became commonplace.