They were popular for a while when Intel and Microsoft were pushing using a USB flash drive as a cache for the HDD. You could leave it plugged in all the time without any risk of accidentally removing it. But the SSDs came way down in price.
Nowadays, the main use is probably for security dongles - a dongle that's needed for a certain program to run or function. You want them plugged into the computer all the time, and you don't want someone to just pull it out and take it. So put it inside the case, and lock the case shut.