The problem is the deer. They just won't spread themselves out! Stupid deer...
Deer will concentrate in one area and be almost nonexistent a couple of miles away. The state cannot micromanage on that scale. In addition, hunters on one property may have completely different harvest goals than the hunters on a neighboring property. The state can't manage at that level. And the worst thing the state could do would be to manage for the worst possible scenario. That would severely limit proper biologically sound management in many areas. The best the state can do is manage for the "middle ground," and I think they're doing a pretty good job of that.
Now I'm not going to argue that the 3 doe/per day limit is necessary. It is not. They could go with 5 does per year and few hunters would be limited in what they are currently taking. That said, there is little indication hunters are over-harvesting does in widespread areas. Since most counties are showing more bucks than does being killed, and there's no indication we're killing too many bucks, then more does could be killed than we are currently killing without doing harm to the overall resource.