Currently there is no benefit to having positive faction with the Far Seas Trading Company.
As you go through the game you will discover that you will gain (or lose) faction with various groups. Having positive faction with some groups stops you being "Kill on Sight" with them, other groups give out quests if you positive faction.
Currently the best groups to have faction with are the city ones as you can gain access to their merchants.
Gaining faction with either the "Hand of Marr" or the "Brotherhood of Night" in Nektulos forest gives you access to the merchants in the camp who have items which are not sold anywhere else.
If you would like a title to display after your name, raise your faction with either the Nybright family, the Drednever Expedition or the Ashen order(or disciples)and a few more.
For a title before your name, doing guild writs for the city factions is the way to go, sadly they make you pay for them.