In most desktop applications, not separating partitions is no biggie, especially on a smaller drive. If you have a large system (e.g. a server or high-end workstation) with multiple physical drives, or a few huge capacity drives, then it might make sense to develop a partitioning scheme specific to the type of work done on the system. /usr could easily be one of those partitions with good reason.
As with most things, though, this turns out to be something that takes a bit of thought to get right, and it's different for different work environments. Also, the more exotic the partitioning scheme gets, the more work it takes to keep it running smoothly. It's all about what works best for your environment and the efficient use of your resources.
Just as an example, when I set up my laptop (with a Hitachi 500 GB drive), I accepted the default partitioning scheme during the install and let it run. Here's what I wound up with:
/dev/sda1 = 12 gigs, ext4, mounted on /
/dev/sda5 = 3.8 gigs, swap, mounted as swap
/dev/sda6 = 449 gigs, ext4, mounted on /home
So it would seem that the default installation procedure finds good reason to create a partition for /home and for swap, but not for /usr. Different systems with different drives and RAM loads will naturally have different results.