Can someone either explain how this is a good idea?
Joel Spolsky did this blog post which I would roughly sum up as "because people are pettifogging separatists and you can't change them". Of course there are legitimate reasons for forking - especially if you consider that a site's reputation is not just a number. But I agree with you that the current implementation makes life more difficult for those with several areas of expertise or interest.
Failing a good explaination, could we stop the madness?
Probably not. As there is little we can do about the forking, I would suggest solving the problem by "finding the right tools". May it be some meta-site which consolidates questions from your favorite tags and sites or an Über-RSS-reader doing the same for you.
Personally, I admit not having put much effort into research on this topic - although I also have the common problem of being interested in security.SE / dba.SE or unix.SE content but at the same time being too lazy and too time-constrained to check the sites separately.