It's an inconvenience, but not a major one thanks to several transfer tools. You'll be able to transfer your contacts to a new or existing Microsoft account, as well as chat history, Credit, and more. There's a guide that will walk you through the whole process.
The bigger question is why. Well, according to Microsoft, it's to “streamline all skype logins”.
“Using a Microsoft Account will enable you to login-in via single sign-in, unlocking all your Microsoft services – including Skype, Office Online, Outlook, OneNote, OneDrive, and more – in one experience, with just one password,” a spokesperson explained. “Currently, using your Facebook account to sign in to Skype is not supported on Skype for Windows 10, the new Skype for Android and iPhone, and the new Skype for Windows, Mac, and Linux.”
As a result, users of the newer clients won't really see a change. It's mostly those who signed up years ago who will be affected, and even there it's not clear how many make use of the feature.
However, as Thurrott's Brad Sams points out, it doesn't feel like we're getting the whole picture here. Removing the feature could discourage new users who don't want to create yet another account from scratch.
It's likely that using Facebook to sign in gives the social media giant access to some kind of information. With Facebook's Messenger and WhatsApp becoming increasingly popular for voice and video calls, that may not be information Microsoft wants it to have.
Of course, that's pure speculation, but it would also be a logical business decision.
You find out how to migrate your account here.