Skype has launched its teacher directory and explains its purpose at this web site: http://education.skype.com/about. Skype in the Classroom encourages teachers to connect their students globally using this free tool. Skype says that there will not be pop-ups or calls interrupted with advertising.
Understandably, this site has bills to pay so it must have a revenue source in order to keep the site free for educational purposes. So don't be surprised if you are using Skype in your classroom and suddenly some advertising appears.