At my work we use a lot of Spartan 3E 1600s and the bit files are somewhere around 1.6 megabytes....  No idea how large the bit files are for the 6 series....  USB could definitely handle it - but then you have to also think about the uC being able to handle it in a reasonable amount of time too.

From what I've seen typically for every FPGA you would have a SPI flash memory for holding the programming - and on boot, the FPGA's bootloader can be told to talk to the SPI flash chip and unload it's programming from there.

I was dabbling around with some code to field-upgrade the firmware in the flash and the Spartan 3E itself doesn't even have enough BRAM to hold the entire flash image on the FPGA itself - I'm going to have to go down the road of possibly having two flash chips, one with some "bootloader" code and the other with the actual running program - and to field upgrade the firmware, I would have code that would be able to access the 2nd flash to write directly to it.

But I guess if you program the chips through the USB comm interface that's 1 less part you'll need ( flash memory ), but it also means much more complicated uC code to be able deal with programming the FPGAs.  And it also means that if the device loses power, that it would need to be reprogrammed again - and the software communicating through USB would need to be able to catch this, or be restarted.  I guess it could work, but in my mind it just sounds kind of hacky.