The Canadian side conceded in the 10th minute to Dwayne De Rosario before Bobby Convey levelled on the hour-mark in the 1-1 draw at RFK Stadium.
Robert Earnshaw could have given TFC all three points when a late chance went begging leaving Nelsen to ponder what could have been.
"I'm really disappointed we didn't take all three points, especially with the glorious chance that Earnshaw had at the end," Nelsen told MLSsoccer.com.
"I'm happy because we were away from home and came from a goal down to get a result, but I'm a wee bit disappointed that we didn't take all three, because I thought the team deserved it.
"When you concede a world-class goal like that away from home, it takes a lot of character to come back. I really thought that we controlled the play for large periods of the game and had the better of the opportunities in front of goal."
The draw left Toronto second bottom on the Eastern Conference table, seven points ahead of bottom-placed DC.