5,832 watched the final home league game of the season at Sixfields on Saturday as the Cobblers drew 1-1 against a Gillingham side who now cannot make the play-offs.
"I thought it was a bit of a burst balloon today," Boothroyd told BBC Radio Northampton.
"I expected us to do better."
With only next weekend's trip to Rotherham to come, Town have 47 points and, despite an improvement under Boothroyd that has dragged them to safety, know that the hard work starts now.
"When we have games like this it highlights that we are not far away but it also highlights what we need to do," added the manager.
"I want a full pre-season and I want them much, much fitter.
"I want to get a more athletic vibe around the place I want us to be fit and out-run teams and score goals late."