The central figure is john brown. why does the artist depict him as such a large figure, and why is he standing between the two sides?

I wager you're talking about Tragic Prelude, the mural painted by John Steuart Curry.

To answer your question: Curry probably had Brown stand between the two sides to emphasize the increasing divide between the North and the South of the United States during this period, a divide that has only grown due to Brown's actions at Harpers Ferry.  

Curry also probably represented Brown as such a large figure to highlight his importance in the leadup to the Civil War.  He is also represented as a fanatic who would kill and be killed for his beliefs.

a. always outside of government control.