Skype used to use an ecrypted, peer-to-peer protocol that made it very difficult for Skype communications to be wiretapped, causing difficulties for the NSA etc.
As per http://www.theregister.co.uk/2009/02/12/nsa_offers_billions_... and similar coverage years ago, Microsoft then bought out Skype even though it was clear it was non-profitable. The peer-to-peer Skype system was dropped shortly after, and all Skype communications were centralized through Microsoft servers.
Following releases by Snowden, it is now clear that Microsoft is wiretapping all Skype communications at the request of the NSA.