I would guess because 3.5” disks were prominent in PCs for much longer than 5.25” disks. When USB was introduced, it would be common for the PC to include a 3.

I would guess because 3.5” disks were prominent in PCs for much longer than 5.25” disks. When USB was introduced, it would be common for the PC to include a 3.5” disk drive but 5.25” had been out of favor for some time by then. On top of that it was common for drivers to be included on 3.5” that came with hardware, even for server grade hardware, this persisted for a long time. It was not uncommon even in the late 2000s for rack mount servers to include floppy drives for this reason. Lastly, because of their size 5.25” disks were rarely included in laptops and portables once 3.5” disks became available. Having 3.5” disks being prominent in laptops led to many miniaturized versions of the 3.5” mechanisms which translate well into a USB peripheral form factor.