And which point of the protocol allows Chile to build a military base there?

The base was established in 1969, the protocol was signed in 1991 and entered into force in 1998.

So why is it still there? They should pack up theirs stuff and go back home in 1998 at the latest.

Because its largely a scientific/meteorological research station and an airport serving that station and the many others of different countries on King George Island, and because nothing in the Protocol prohibits it?