Would you expect the host device to know the internal layout properties and hardware limitations of a purely passive bank of flash memory (e.g. when to mark a sector as failed)? It's possible but distributing the hardware and software to do this effectively would be a very difficult problem, and industry standardisation to mitigate it would be hard to arrive at as well, and deploying advances in flash memory would be hampered (remember when people worried about 720kb/1.44mb floppies? Imagine that for each new generation of flash memory. Is your flash drive slot MLC NAND flash capable? NOR flash? TLC? HKMG?)
Instead we live in a world where not just thumb drives, but even memory sticks and SD cards, are active devices. (This is, of course, to say nothing of the convenience of using one port for everything.)
I guess not making it an universal bus is one of the steps for that. Also, making it either optical or magnetic should help.
Plugging in USB is just as unsafe as about anything else you can use a computer for.