The Cobblers have now gone four games without a goal despite pressing for a breakthrough for most of the match, with Adebayo Akinfenwa coming closest when his header hit the bar.
As a result, they are now four points behind third-placed Rotherham United with just two games left and it looks as if they will have to settle for a play-off place.
Boothroyd said: "I thought it was a very good performance. We mixed it up well and I thought Luke Guttridge and Lewis Hornby did very well coming back into the team.
"I've been scratching my head at some points of our away performances where I've wondered if we're ever going to have a shot away from home.
"But tonight I thought we did everything but score and on another night we win that 3-0 or 4-0.
"The important thing tonight was to keep a clean sheet, to wipe the blood off our nose from Saturday and to put in a good performance and I felt we did that.
"It's very rarely you come away from home and have a team on the back foot as we did tonight.
"We were going for it and the lads are very disappointed, but I know that over time if we play like that we'll win a lot more than we lose."