I spoke with David a few months ago. He said that the percentage was based on the number of active websites, which according to http://www.whois.sc/internet-statistics/ is 139,902,673.

I don't know for sure if Weebly uses this number to calculate the percentage. But probably not, since it only indicates ~2.8 million Weebly websites, and they claim 11 million (7.8% of that active domain number).