You should be able to hook up an amp to an mp3 player interface. A lot of them are basically just RCA cables (for your amp) that have a headphone jack (for your mp3 player) and an additional wire that will recognize a signal and turn your amp on and off. The only problem that I can see with just running a thumb drive for your tunes, is that you'd have no user interface. As in, no way to see what's playing, or control it.
I'm about 95% sure that you can find the stuff pretty cheap to hook up an amp and speakers to just an mp3 player. You'll have to use the mp3 player to control the volume, which song, and stuff like that though.
I'd check with crutchfield.com that's where I bought something similar for my boat.