What were the traveling practices of merchants, roughly between the Middle Ages and the Renaissance?

I would recommend a read through Janet Abu-Lughod's book, Before European Hegemony. This covers trade routes and practices in different areas of the world during the late 14th through early 16th centuries. The remainder of this answer is pulled in great part from what I understood of the book.

Water ways are preferred due to a lower rate of banditry. While piracy was common in the Mediterranean, it wasn't as common in the Indian Ocean. The Italians, particularly the Genoese and the Venetians, would have a convoy to protect the merchandise and harried each other's ships.

Numbers mean a lot. Most pirate enterprises can't afford more than one ship and joint operations are difficult to orchestrate. Whenever you get two different groups with two different goals, e.g., "Whose purse are we filling?" you end up with a separation of interest. If a merchant convoy is large enough, it would be a significant deterrent to a pirate with only one or two ships.

Land routes don't have such simple limitations. People are typically land-bound; that's our natural habitat. We don't need to have a ship to carry loads on land. We don't need to have a ship to afford us shelter on land. Because of this, it is much easier to have a larger band with which to attach merchant convoys. Thus, land routes had a higher rate of banditry and it would take greater numbers to deter bandit attacks.

Why are deserts safer? The deserts are harder on travel and sustenance. If you're traveling through the desert, you're traveling with enough to sustain your journey to the next watering hole or trade post. If you're a bandit in the desert, it's more difficult to sustain yourself between raids.

During the late 13th and early 14th centuries, there were four towns in the area of Champagne which had regularly scheduled and rotating fairs. The fair would stay in each town for a couple of months before moving to the next. Each town encouraged trade of particular wares, so merchants interested in buying or selling particular items would know when to be where. For the fairs to be successful, the lords of these towns and their surrounding areas had to secure the safety of the merchants traveling to the fairs. When this guarantee was no longer provided, the merchants sought other venues.

Europe was behind the times, though. Note that the title of the book clearly indicates a time before Europe dominated world trade. The Italians, being closer to the traders from the Middle East (and discouraging direct trade between the rest of Europe and the Middle East), were more familiar with many of the trading practices of the Middle East. This included loan instruments and various forms of housekeeping.

Often, there would be a partnership between merchants. The one partner, usually the one with more invested financially, would stay in a shop or warehouse in the home town while the less invested financially would invest his safety into acquiring and transporting goods.

In the Indian Ocean, there were a few cities that became merchant cities. The weather patterns in the Indian Ocean prescribed travel in particular directions. Merchants could only practically travel east in the spring and west in the fall. During the summer, they would set up shop in the area of Sumatra and, during the winter, set up shop near the straits leading either into the Persian Gulf or the Red Sea.

In short, the book covers key elements to a healthy economy and illustrates them several times. A healthy economy requires safety at home, safety to produce materials beyond what is necessary to subsist. A healthy economy requires safety along trade routes, safety to travel to a buyer willing to purchase your excess. A healthy economy requires a consistent schedule, safety to know that, when you get to your buyer, your buyer will be able to purchase your excess.