I suppose you could tap into the USB voltage source, but I'm not sure how much current you can draw from it before your mobo resets... You should, however, read the specs of the fan (max power, current, etc...) and use a volt-meter to read the voltage (making sure that it is within the range specified by the manufacturer. If it is from the USB it is probably 5 volts.) I am not sure if you have to worry about shit like inductance with a DC Fan (most DC motors would require that you do) and if it would have a serious effect on the sensitive motherboard signals (or the device connected to the USB port.)
Also, if it draws a lot of current, consider placing a resistor or something, it could have some impact on your battery life.