The answer to transparency of the lens proteins and, in turn, the lens as a whole lies in a few concepts:
1) The crystallin proteins found within the lens are packed/configured in such a way to promote transparency. This idea is quite similar to the organization of collagen fibers within the cornea.
2) The lens maintains a decent amount of metabolic activity in order to maintain its transparency.
3) Mature lens fibers lack organelles like a nucleus and mitochondria which would reduce transparency.
It’s important to note, though, that many would argue that the lens starts to lose a small amount of transparency each day we are alive. As the lens thickens over time with the addition of fibers, more and more light actually does get absorbed and/or scattered. This is the natural process of cataract development