330 or 390 or even 470ohm are good numbers in that they work for a variety of situations and are fool prove: they work for npn / led @ 5v / 3v, under 10ma or 20ma drive; they work for led @ 5v/3v under 4ma drive; they work for mosfet (slow speed); and you can short them safely, ...
They also work for high speed input too: their cut-off frequency with a typical avr pin is 70Mhz, far higher than most practical applications.
It is just a good all around number.