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Each dot on the map represents an entry in the listings. At the overview level, it gives a good indication of the geographic distribution of listed buildings. Zoomed in, you can click on the individual dots to take you to the page for that entry.
Note that Historic Scotland's categorisation criteria are different to those used in England and Wales, so the larger proportion of yellow and blue markers in Scotland doesn't mean that Scotland necessarily has better historic buildings - they are just classified differently.
This is an experimental map using Google Fusion Tables to display the location of (almost) every listed building in Great Britain. It has a few known issues, including the fact that the markers are sometimes not clickable, and there are some buildings missing.
These are limitations of Fusion Tables, and not something I can fix here. But there are no other freely available mapping products capable of displaying upwards of half a million markers on one page, so it's still better than nothing.