Co-founder and CEO Niklas Zennström is a Swede and so Skype always had a clear connection to Sweden. But yes, Estonia also deserves a lot of credit for Skype of course, as the development work was mostly done there.
A lot of the credit? Estonia is 99% of Skype. There's a reason their tech ecosystem (which is more impressive than Sweden's) is called the "Skype Mafia"
Anyway, my point is that whether correctly or incorrectly, that thanks to Zennström, many people do associate Skype also with Sweden, and he acted as an early role model for other future startup entrepreneurs from Sweden.
