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 lengthactual 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.