I've answered a similar Question: Does the number of downloads displayed for a plug-in in the WordPress.org plug-in directory include automatic updates?
This is Otto's blog post in make.wordpress.org with plenty of information about this stats.
Excerpts from the whole page (article and comments), worth reading in full:
First, on the extend plugin directory, you may notice some new pie chart fun on the stats tab for each plugin. This shows a percentage breakdown of the versions being actively used by that plugin’s users. Only slices greater than 1.0% are shown.
[...] it’s saving the total counts of the version numbers as reported by the plugin update-checks over the last week. Since the data at present is only from one day, it’s not very accurate.
[...] the download count includes direct downloads as well
[...] There is no “raw count” anywhere on that version number chart. The raw count is not data that will be made available.
The numbers come from the sites where it is activated, not just installed.