AT put his finger on the issue.
Early on, one places cottages near rivers to tech faster.
The watermills, windmills and workshops are not very attractive when they first appear.
In newly conquered cities during the riflemen and beyond stage, it would take too long to develop those cottages for new cities.
Building watermills, windmills and workshops yeild an immediate benefit.
Also, I have built cities on plains/hills for their double production and hill defense, even though I didn't have plenty of food. Later, I add windmills to the surrounding hills to grow the city and gain a gold/turn from each.
I have played a lot of 'always war' and 'raging barbarians' games and plains/hills are your friend. Being able to utilize your archer's natural hill defense bonus, plus the hill itself, can save you when attacked in masse.