The Robins could have scored several times in a promising opening 45 minutes at Glanford Park before they faded badly in the second-half.
However, Allen, whose side have already been confirmed as relegated, preferred to take the positives out of the game.
"I thought our team were absolutely outstanding, to be honest," he told his club's official website. "In the first half we had four great chances to go ahead and we even created some chances near the end.
"It's frustrating to see the 3-0 scoreline but there was more to it than that because we had to give some experience to some players who are going to be the future of the club.
"I've said to all our young players that now they've had a taste of it, they have to work really hard over the summer to challenge the pros for the first-team spots."