Are you selecting the usb device as the source? I ask because I use an I-pod and have a Samsung phone, both connected via Bluetooth and sometimes it recognizes the phone only as the source for phone and music, and then I have to select the I-pod for the music source.
check out this thread:
http://www.toyota-4runner.org/5th-gen-t4rs/65621-how-use-usb-hard-drive-music.html
you will need a utility to format a USB drive larger than 32gb to fat 16/32.
I followed this thread a long time ago and it worked perfectly for me