Linux doesn't have a problem with USB in general, I'm currently typing on a USB keyboad and using a USB mouse and using USB sticks is just as easy as Windows. The only problem I've heard about is that some hardware (whether it be USB or otherwise) isn't Linux compatible.
I don't blame the Linux developers that some hardware won't work under their OS; it isn't fault that the hardware companies won't release drivers for their OS and choose to keep their protocol proprietary any drivers they do produce are a product of reverse engineering.
Also, I've heard that Vista often has a problem with drivers and I know that Windows XP does. I have an old Canon LBP-660 printer that doesn't have an XP driver so I use the Windows 2000 driver which isn't perfect, it tends to not allow switching between user accounts so the first user that uses it loack everyone else out, the onlly solution is to reboot which is a pain in the neck.
I would say that if you want to use Linux, only buy hardware that's compatible with it, you wouldn't install Mac OS X on any PC would you/?
The next PC I get will be a Linux PC and I'll select the printer, scanner and everything else to be Linux compatible so I don't have any problems.