Former Newcastle defender Hughes was forced off with an injury after 77 minutes to be replaced by the inexperienced full-back Toni Kallio and it was the substitute who was out-muscled by Jason Roberts for Rovers' winner.
And Hodgson felt that change led Fulham to concede the late winner.
"We were unlucky to lose Aaron Hughes in the last 15-20 minutes," he said. "It wasn't easy for Tony Kallio, who is not a natural centre back, to come in - we've got (Chris) Baird out injured and he would have been the ideal man in that kind of situation - and of course Kallio got rolled for the goal.
"We would have liked to have thought we would have got at least one point from the game."
No excusesHowever, Hodgson made few excuses and thought his former club deserved their victory.
"I've got to say I thought Blackburn played with a lot of energy. We were struggling to match that energy," he added.
"There have been a lot of games for us recently and players are beginning to look tired.
"They've played the long-ball game very well and forced us back.
"I can't say they didn't deserve to win the game, I can't say that we did enough to win it. We lacked a bit of energy but the lads put up a brave performance.
"We simply met a Blackburn team with more energy than us, more strength than us and as a result they were able to get the three points which were so vital for them. We'll just have to wait for ours."