why can it fry my arduino?
Low (dc) resistance isn't the issue: you can actually short your avr's pins without damaging them.
Motors are inductors who will try the best to sustain its status quote. If the current going through it is cut off, it will create a significant voltage trying to sustain that current. That voltage is higher if the cut-off is quicker.
So w hen your io pins turn off fast, that huge voltage is applied to the pin -> causing it to go to the avr heaven.