But Colchester earned a share of the spoils when they equalised two minutes later through John-Joe O'Toole.
Boothroyd said: "We did not play very well at all. We were slow getting started. We thought we were going to walk away with it against a struggling side and it was a wake-up call for us.
"It was tit for tat in the second half when we should have won it, but in the end we were grateful for a point.
"We were a little bit disjointed at times and we made some mistakes. Their goal was no surprise. They put us under a lot of pressure but it was a good response from us to get back level so quickly."