Mostly because the colonies became colonies at different points in time and had wildly different cultures and societies. Most colonies, such as the Massachusetts Bay Colony, became colonies some time after the Glorious Revolution, when King James II revoked charters and royalized the colonies, with similar stories throughout the US. Individual colonies relied on localized government (before passage of the Intolerable Acts later on) and were for the most part self-governing, with the occasional order or law passed from England.

A single large colony would have likely been too large to govern effectively, and the religious and economic differences between the North and the South, even in that period, were such that a single colony would have been bloated and inefficient. (Sorry for the speculation).

Source: Chapter 3," An Enduring Vision: A History of the American People" (Fifth Edition, Boyer).

There were more than 13 original British colonies in North America. Newfoundland, Nova Scotia, and Rupert's Land were all British. Even Quebec was technically British in 1776.

The reason why there were so many colonies was because of how the charters were distributed. The initial charters were for the Plymouth and Virginia colonies. These were defined and separated by King James I. He also ordered that there be no settlements between the two colonies in a 100 mile buffer that represents what is now known as Delaware through and New York State. The crown then gave away new colonies such as Maryland, Connecticut, New Hampshire, Carolina, and Rhode Island to people they knew or as they saw fit.. After the third Anglo-Dutch War, the English took over what was referred to as New Netherlands (NY, NJ, Delaware, and parts of Long Island.) These were then separated into separate colonies.

Each colony had a different lifestyle and history. Virginia and the Carolinas had fewer towns and mostly large plantation systems set up that required slaves to work them. New England had farms and commerce, along with fishing industries. New York was a huge out post for trading with the Indians. As such, each wanted independence from other colonies so they could govern them self as they felt they needed to be governed. Given that England was mostly at war or pre-occupied with other events this served the purpose of leaving all the colonies separate. And colonialists in America were given huge liberties with self government that would happen in Europe, so they wanted to maintain that power structure.

That was until James II decided to enlarge New England and have it contain all of New England, New York, and the Jerseys. This lasted a short amount of time before the Glorious Revolution stopped it. It was not until the Congress of Albany in 1754 where the English said that the colonies should consider a united colonial government structure. Twenty years later it happened.

A few more things. There were actually more than 13 colonies. Some colonies never lasted and were absorbed by others. New Haven was a colony that tried to be independent but was taken over by Connecticut in the late 17th century. Stamford Colony as well. And Massachusetts Bay took over the entire colony of Maine and it was part of Massachusetts for over 100 years.

Most of the above can be found in Murray Rothbard's Conceived in Liberty. This is a free text book that also exists in audiobook format that can be downloaded here.