Everyone in the class is silence.

Everyone in the class is silence.

Everyone in the class is a good student.

I presume the first of the above two does work. I think you mean doesn't, not does.

But how do you explain away that it doesn't work while the second sentence with a similar pattern does sound right and good.

It's not the same pattern. #1 has an uncountable noun, while #2 does not.

If you replaced uncountable with countable, the #1 sentence would be correct grammar,

eg Everyone in the class is an umbrella.

Howver, as you can see, the meaning would not necessarily make sense.   

Best wishes, Clive