It's the circle of life, you plant apples, deer come, you shoot the deer, you now have 2 things to eat...
Fence it in, unless your area is polluted with bears, should not be a problem. My co-workers all live in an area in NY with a lot of bears, garbage marauding is an issue during the early spring. In the fall, they rarely see bears around the house. Given that's when apples come into season, that should be a good indicator. The fall is rich with food sources, so animals tend not to get into trouble with sources close to homes.