i may not be understanding what you're misunderstanding at all. if so, sorry!
i'm sure you know that trade routes are what you see in the upper left of your city screen. once you have a trade route connection between your cities or with another civ, the game automatically picks the most profitable ones between your cities according to whatever the rules are (i don't know what they are, i just let it do the magic).
then there's a command like "build trade network" for workers. it will hook up resources, and build roads between your cities. but one connection between cities is enough as far as trade routes are concerned -- road, river (only after sailing in BtS), coast (post-Sailing), ocean (post-Astro). what the workers do for a trade
network, and the existence of trade
routes, aren't directly connected except that it'll have the workers build the roads for you.
if you're talking about
this article, it has nothing at all to do with workers except that the cities need a path to each other, and often that involves building a road. you won't get better trade routes by using your workers to build a trade network
if you already have all your cities connected to each other and to all civs you have OB with. they'll hook up resources you haven't hooked up yet, which can give you stuff to trade, so that's spiffy.
once there is a connection, the game sorts out the trade
routes automagically. if a new city possibility pops up (you find/build a new connection, you open borders with somebody else, you or an OB partner build a new city) then it'll change which city's connected to which behind the scenes. which is good, since my brain can't handle all that math.
i think the trade network command makes extra roads, more than you need just for the trade routes. i think it puts roads on most tiles? i'm not sure, i don't use it myself but i see lots of roads in the AI lands and they have to use automated workers so that's my guess. but there are plenty of other reasons to have extra roads so it's not necessarily a horrible thing.