When I open a file in Illustrator CC 2014 that doesn't have all the fonts it needs enabled, I get this message. But I am. I was able to browse and add a font from Typekit when I first encountered this error. I am able to install updates, etc. Everything else seems to work fine.
I do have Font Agent Pro installed, but haven't looked for updated plugins yet in part because I only just realized that the 2014 update installed as completely separate installs which is kind of annoying. I guess it avoids plugin conflicts, but if that's the concern, just move them to a disabled folder rather than consuming more hard drive space. As it is, I still have a CS5 install I need to figure out how to remove at some point.
I'm sorry that you ran into trouble with this. The error is actually coming from the InDesign application; it just happens to appear underneath the Typekit logo in the missing fonts dialog box.
If you go to the Help menu in InDesign, you should see an option to Sign In:
If that doesn't fix the problem for you, the InDesign forum should be able to help further:
I hope that this helps,