Town took the lead through Jay Tabb, who scored on his return to Reading, but could not make the most of some good chances.
Reading made them pay for their profligacy with a 75th-minute winner.
McCarthy told BBC Sport: "[I'm] hugely disappointed with the result, but buoyed, encouraged and proud of the performance.
"They had the possession of the ball but without any chances early on. Once we sussed out our shape against theirs, I thought we were the better side. Arguably we could have been more in front.
"It wasn't justice going in 1-1, and even more so to have lost the game to a deflection."
McCarthy, who praised the performance of debutant Tabb, also said there was plenty to "take heart from".
"After the game you're sort of down in the dumps because we've been beaten - and I am. But I'm really proud of that performance," he added.
Ipswich sit in 17th position after today's results.