Excellent question!
In terms of where fortified settlements are found, prominent hills that provide for better defense, natural harbors on the coasts, good crossing points of navigable rivers, and points on overland trade routes (as well as crossroads) are all good candidates.
For example, the city of Florence prospered in no small part because it was positioned right on the overland trade route between Venice and Rome, and on the overland trade routes from Italy to northern Europe. So in a sense, roads helped to build the city…although Florence’s growing industries in wool cloth, silks, and finance then gave reasons to build roads to connect other places to Florence.

In terms of what factors decide where roads go, it really comes down to geography (in the sense that a lot of main roads get built to connect major regions – think about the Via Appia, which the Romans built to connect Rome to connect the capitol to the grain-growing regions of southern Italy – or to deal with major natural obstacles (think roads built through mountain passes or bridges or the like)),and demography (in the sense that when you have clusters of people (because they’ve found a spot with certain advantages) it generally makes sense to build roads to connect them so that trade can be conducted, and this in turn makes those clusters bigger because it’s easier to move to those clusters, and creates new clusters at key points of the new networks).