Pompey matched their hosts until the 61st minute when James Collins opened the floodgates and the striker went on to score another three, with Danny Hollands also getting on the scoresheet.
Whittingham said: "For an hour this was our most organised football for a long time and we were doing well. We were frustrating Swindon.
"Our game plan was going well but the third substitute made by Swindon when Collins came on the stadium erupted.
"Our team is made up mostly of young kids waiting to make a career and hopefully they will have learned from this defeat.
"On paper it looks like we have been crushed but the scoreline does not tell the whole story."