Problem:

I've always thought that the majority of the "work" in a cell is protein production, until I read the following.

The Wikipedia article on the central dogma of molecular biology states this:

80% of the human genome is transcribed even though only 1% codes for proteins.

and this:

Current research focuses on investigating the function of non-coding RNA, that is, RNA that does not follow the dogma trend and does not code for polypeptides.

If 99% of what's transcribed isn't used for creating proteins, what is it used for? If it's not known - are there any hypotheses?

Any ideas? Or better yet, pointers to places where this has already been answered?