Based on my experience, I believe it's to continually draw air through the enclosure:
I too doubted the usefulness of it, and when delivered, my SD4 even had a 'coffee filter-like' material covering it, which I removed. (I don't seem to have an ABS odor problem like some users report, I'm not sure the filter would have solved that anyway) At one point during my tweaking, I disconnected that fan, thinking I wanted to keep my enclosure at a warmer temperature, with no airflow.
In playing with bridges, overhangs, etc., I decided that if the temperature inside the enclosure is TOO warm, my nozzle fan is just blowing hot air on the filament as it exits, and isn't cooling it nearly as well. I subsequently re-connected the fan, and noticed improvement in overhangs, etc...especially with PLA. You can see this on my Christmas ornament in the Print Showoff topic; that ball-ornament with a scene inside is an 18-hour print at .1mm, with NO support material.
I've come to the opinion that the purpose of the enclosure is to mitigate sudden changes in room temperature, and airflow is not necessarily a bad thing. I would guess that this varies with the room environment the printer's in.