There is an extension to your agent that will increase your positive rep and descrease your negative rep for each point you put in it.  I don't remember what it's called, but it's above the extension that lets you run multiple parallel missions.

I don't know what kind of overall impact this has though.  Is it even worth putting points into?  I mostly run transport missions, so I put points in it...I'll be running transport for all the factions.  Overall, my reputation should increase across the board, even if it's slowly.