The overwhelming silence in shy classes
I think the best way to deal with this as an instructor is to set the tone right from the first day.


Make it clear you want an interactive class room, and that includes the students asking questions and even challenging you as well as having the students answer your questions. 
Make sure your questions are worth answering. No one wants to answer an obvious question that was in the book they read for the day ("How may valence electrons does an oxygen atom have?"). Students like questions where they have to think a bit or interpret a bit. 
Conversely, make sure your questions are not too hard, and that they are not unclear.
If all else fails -- and it often does the first time you ask an interesting question on the first day of class -- this is what I do. I wait a moment, then smile and acknowledge the awkward silence. And then I let the class know that I want an interactive class and that I'm perfectly happy to stand at the front the room through the awkward silence for as long as it takes. From my tone, I make it very clear that this not me being strict and judgemental, but that I want to work with them and that's why I am doing this.