1. There were over 200 settlers who made their home in Jamestown, but that number later dwindled to a little over 50. During a period known as "the Starving Time," food supplies dwindled due to a poor harvest. There is some historical evidence of cannibalism among the colonists.
2. The location of Jamestown and the early settlements of the Colony of Virginia was not ideal. There was little game to hunt and much of the water was brackish.
3. In the early days of Virginia, there were financial hardships. Early settlers had hoped to find precious metals, such as gold. They had not intended to be farmers. They attempted to grow crops, but were often met with failure. With very little to export, the Colony was not financially viable for some time.
4. Those who survived during the Starving Time nearly abandoned the Colony. In addition to a lack of food, there were also conflicts with the local Native Americans. They were prepared to leave Virginia entirely when a supply ship arrived.
5. The early settlers of Virginia were mostly men. When women did arrive, there was still a sharp unbalance. Disease and other hardships were common in Virginia, and some women died after arrival. It took decades for there to be a more balanced amount of women and men.
It certainly wasn't the best place they could have chosen to land, and the fact they had been on the ocean for weeks no doubt influenced their decision.
Much of the colony was a swamp, which bred huge swarms of mosquitoes and invited malaria. It was also difficult to farm those regions without first draining them.
The land was undeveloped, and had to be hacked out of the wilderness.
Relations with the Native tribes were often testy at best, and it made it difficult to increase settlement on the frontier.
It was difficult to get labor to the colony. Indentures were expensive and temporary, and slaves had to be imported from long distances.
It was difficult to convince women to settle there, and this made male settlers restless, in part causing Bacon's Rebellion.