We just returned from a great week at Fort Wilderness. Our cabin number was 2103 which was near the front of the 2100 (Bobcat Bend) loop closest to the center of the campground. The bus stop was just across the street from the front of the loop, yet we were not bothered at all by bus noise. Although we had a cart for 5 of the 7 days (which was very convenient and the kids really enjoyed it!) our location was an easy walk to the Meadow Trading Post, Bike Barn, pool, and campfire area.
I would highly recommend the 2100 loop, and you could specifically request to be near the front of the loop to be near the bus stop.