1. The complexity of the USB protocol enables certain kinds of attacks that aren't possible through a floppy interface.
2. The circuitry present in a USB drive is capable of being partially replaced with other kinds of circuits in a hard-to-detect way, whereas, it's pretty easy to verify that a floppy disk contains no malicious circuits.
These two vectors can be combined (along with other vulns) to do things like momentarily connect an unexpected modem to computers that are thought to be airgapped. (There are other, simpler, attacks such as having it exfiltrate data to a secret portion of the flash memory at the same time the drive is operating "as expected", by simply connecting itself as two devices.)
This isn't a problem for most people, but it's entirely possible that there are materials at the White House which need to resist this level of sophisticated, can-create-our-own-silicon-with-hidden-radios level of attack.
Remember, the NSA catalog was full of ordinary seeming devices that were meant to exfiltrate data or create radio links in to the computer.
If Sony's payroll, upcoming scripts, etc had been stored on floppies, stored in a safe when not in use, they could have saved themselves a lot of embarrassment.
For certain kinds of highly sensitive information transport, a floppy disk is probably a better idea than a flash drive.
I suppose you could use CDs, but floppy disks seem easier to destroy.