You can see right through something transparent. A window is transparent, but so are the intentions of a Peeping Tom looking through that window.
Obviously the glass of a window is transparent, but transparency is also a way to describe something that is clearly understood and lacks any deception or secrecy. Reporters use it these days to describe the ideal way for government to develop policy, where voters can see the process and how decisions are achieved. Some in government, however, would argue that the leaking of top-secret information takes it a step too far.