Tolls and taxes were certainly part of it. I'll keep things focused on one period/place (Northern Europe 7th-9th century) and maybe others can give you more on other time periods.

We know that the Carolingians collected tolls on all trade going on in the major trade centers, as there are numerous documents which mention immunities or discounts on those dues for certain figures.

Cities probably also made money on food, lodging, and production of trade goods. Dorestad, the premier trade center in northern europe c. 700- c. 850 was not just a major trade center, they also produced pottery, jewelry etc. for trade.

As to why you wouldn't just "go around", a few reasons.

• Geography: The important trade centers were important because of where they were located. Generally on rivers, which were by far the most convenient means of travel and of moving goods. Occasionally near a very important monastic site (such as St. Denis in Paris) which produced important goods and was wealthy in its own right (and thus a consumer as much as a producer) or at important border sites.

• Laws: In the Carolingian Empire trade was tightly regulated in order to properly channel revenue to the kings and to prevent certain goods (mostly high end Frankish military products) from trickling into certain areas. Trading on any real scale was illegal elsewhere, though certainly small scale trade must have occurred. Also, rulers wanted to encourage trade that they could control so while they might make laws, collect dues and taxes, they also offered things like security and comfort at these sites, which made them worthwhile.

• Connections: Traders want to make money, to do this they need people to sell to and people to buy from. These people congregate in specific places (see 1 and 2), if you skip those places to avoid tolls you also skip the important connections there. Sure you might be able to sell something at a beach side market, but you won't make as much. Trade cities have established institutions (and often colonies of foreign merchants who would help others of their "people" fit in).

Sources:

Georges Duby's The early growth of the european economy is a classic, though perhaps a bit dated.

Richard Hodges has a couple seminal works on this topic: Dark age economics: the origins of towns and trade A.D. 600-1000 and Towns and trade in the age of Charlemagne are both good.

Michael McCormick's [Origins of the European Economy] is a tome but if you don't let the size intimidate you there is interesting stuff there.

Hope that gave you some ideas about the topic.

Trade cities in the ancient Mesopotamian world benefited both economically from tolls and great amounts of trade items. Ancient trade cities like Kanesh in Anatolia, Assur in the Assyrian Empire, Mari and Babylon in the Babylonian Empire, Sidon, Tyre and Byblos in Phoenicia, and Tanis and Avaris in Egypt to name a few benefited greatly because ancient merchants, both land and sea, traded at every market they could. Ancient merchants did so because it was very costly to trade in the ancient world and logistically required a lot of specific conditions to be fulfilled for a successful trading expedition. First, the merchant needed to make sure they could feed their animals that they were riding and using as pack animals or maintain the ships they were using. This made it so they had to plan according how far they could go with the feed they had or how long they could go before their ship had to be repaired at a port. The constant need to feed trade animals and maintain merchant ships left the possibility of many cities on a trade route to acquire many commodities at their market. Second, trade of commodities and exotic items happened at every city on a trade route because every ancient world merchant had to consider constantly what they were trading and how much weight they were carrying. This made it more likely for an ancient merchant to make a deal whenever they could, rather than waiting for one market to make all their trades in. Solely because sometimes it would not be profitable to travel a certain distance to trade some copper when you could trade it at a closer destination. This is was something that the ancient caravan merchants between Assur and Kanesh did in ancient Mesopotamia and something the Phoenicians and Israelites did in the Levant during the Iron and Bronze Age with their maritime merchant fleet. So along with the tolls, all cities on an ancient trade route benefited from trading because even cities that produced lots of agricultural crops and yields could trade their products to get silver from merchants. And this is why cities like Mari in the ancient world were able to form a great city and become wealthy in the middle of Mesopotamia, almost complete isolated from other major cities. Additionally, the second major benefit of living in a city on an ancient trade route was being in a place that fostered cultural and idea exchange.

Being able to live in a major trade city was a huge plus for its leaders and its people because they were able to see all of the products being traded, see all of the new technologies and commercial services being offered, and they were able to hear all the new ideas and stories of the ancient world. The best examples I can give of these are Babylon and Assur in Mesopotamia, Athens in Greece, Byblos and Tyre in Phoenicia, Carthage in North Africa, Syracuse in Sicily, Knossos in Crete, Persepolis in Persia, Neopolis and Rome in Italy, and Alexandria and Giza in Egypt. These were great economically rich centers of the ancient world but they also had signs of being great cultural centers and places where ideas were forming. Babylon became the intellectual center of ancient Mesopotamia that the explored ideas of science, mathematics, and religion. Athens became the birthplace of philosophy and the new form of democracy that the Athenians formed. Alexandria became an intellectual center that trained many Hellenistic Mediterranean scholars and the home of one of the greatest ancient world library, the Library of Alexandria. Tyre became a city of great temples or palaces since there were a collection of great builders and architects that lived there in the Bronze and Iron Age and Persepolis became an architecture wonderland with the first paradises, or gardens, intermixed with great architectural feats for the same reasons. The example of these trade cities show that being on a trade route, either land or maritime, had great benefits both economically and culturally. These benefits of being a successful trade city is why these ancient world cities still resonate in our brains today, with three of them possessing wonders of the ancient world. So ancient trade cities benefited not only from the tolls and the trade products they got from merchants but also from the cultural and technological ideas that were being exchanged in their marketplaces.