USB floppy disk drives can't deal with Amiga formatted discs (it's an hardware limitation of the device itself). Build-in PC/Pegasos floppy disc controllers can't either.
The only way to read AmigaDOS formatted floppy discs is to get a Catweasel PCI Card (btw the MK3 works in read-only mode with MorphOS using the AmigaOS Open-PCI drivers).