Why does atmel use 39R pull-down resistor?
It's not a pull-down in the strictest sense that some other chip may be required to activate said line and fight against it. The chip in the OP's diagram is permanently chip-enabled as far as I can see and this is achieved by the 39 ohm resistor. If it were a zero ohm resistor would anybody quibble?

So why use a 39 ohm resistor instead of a zero ohm resistor - maybe there is another 39 R resistor used elsewhere on the board and they didn't want another line item in their Bill of Material: -



So it seems!