Yep, a lack of knowledge of the Bible definitely means people don't understand various phrases and references in literature, movies and tv shows. It's not just the Bible though. They also miss references to Greek and Norse myths, Aesop's Fables and other stories which used to be staples and as Sarah mentioned there is a lack of reading in general.
When I was studying a foreign language at uni we had a lesson where we were supposed to look at idioms in that language and match them up with phrases in English that meant the same thing, demonstrating the difference between a literal translation and translating the actual meaning. The lesson didn't go well because for this class full of twenty-somethings in a university most of the English idioms were totally unfamiliar and most of those they had heard before they didn't understand. We're talking stuff like "oil on troubled waters" and "sour grapes."
It's a pity to see these ways of speaking and writing disappear, but I suppose new things will take their place. For my part I will try and expose my kids to a wide range of literature to pick up as much vocabulary and general knowledge as they can.