Interesting question! Let's share some background information on Jamestown first.

Jamestown was settled on May 14, 1607 by the Virginia Company from London. It was located about 60 miles south of the mouth of the Chesapeake Bay, and it's location was picked to avoid taking direct bombardments from potential Spanish ships which would have been a serious threat to the settlers.

Jamestown was also England's first permanent colony, but it suffered from many problems from the start. Within days of arriving, the Colonists were attacked by Powhatan Indians. They were plagued with problems throughout the life of the settlement, from increased attacks by Powhatans to issues with disease and famine. However, fights with the local Natives did fluctuate since they reached periods of peace and when open trading was more common, likely saving the lives of many hungry colonists. But things bounced back and forth between positive and negative, with the negative taking the majority of English lives in the colony. the winter of 1609 - 1610 has been referred to as Jamestown's "darkest hour," when the 300 settlers were besieged by Powhatans that winter, with only 60 surviving until the Spring. Some years of peace did take place in the mid 1610s, but by 1619, it was much stronger as a small town.

Jamestown continued to grow at a healthy rate until the end of the 17th century. Jamestown started having an assembly in 1619, and saw influxes of immigration going forward until 1676 when Nathaniel Bacon and his rebellion sacked and burned much of the town, however, Jamestown continued to be Virginia's capital, but did not fully recover from the damage. Hardship hit Jamestown again, and for the last time when a fire destroyed the statehouse in 1698. This led to arguably the biggest factor that led to Jamestown's abandonment was when a new Captail was erected in Williamsburg, which replaced Jamestown as the capital. By the 1750s, the entire area had been overall abandoned by settlers except for two families that had turned it into farmland.

So in summary, Jamestown as a colonial capital was repeatedly hit with hardship over its 90 year history. Because the town was repeatedly attacked, especially by Nathaniel Bacon, and mixed in with the fire that destroyed the state house, there was less and less reasons for people to stay in the area, especially when larger, safer and better locations like Williamsburg popped up.