The basic answer to "why" is: because it doesn't matter in any practical way.
To put it into perspective, this is a 4.8% difference in sensor area. Or, linearly, it's 2.3% difference in crop factor.
This is not very much, and generally other measurement tolerances will be less precise. For example, if you measure the actual focal length of, say, a bunch of different models of 50mm lenses, they probably have a greater variation in field of view.
In general, newer sensor technology moves forward, and in this case there's no exception: the D3100's sensor is significantly better, particularly for controlling noise at high ISOs. From dpreview:
The D3100 offers little to complain about in terms of image quality, and its new 14Mp sensor delivers very good results. High ISO performance is substantially improved over the D3000 [...].
Basically, the small difference in sensor size is insignificant compared to the improvements in terms of image quality, and the small difference in framing is likewise a non-issue.