Former Robins defender Michael Rose drilled in a 70th-minute free-kick that proved enough to earn Colchester's new manager Joe Dunne his second win from as many matches in charge.
Di Canio said: "This is the first time I have not been angry after a game but I am not surprised and we will be in training on Wednesday.
"Enthusiasm, passion and desire is more important than the system I play.
"I said at half-time 'defend and we can get a draw' but we had no passion or desire.
"We learnt from this game and to get the way I want the team to play we will have to work hard."