Rovers went out of Europe at the first-round stage for the third time in five years after drawing 2-2 in France on Tuesday and losing 3-2 on aggregate. Blackburn have won just one game all season and are currently two places off the foot of the Premiership after being among the front- runners 12 months ago.
Hodgson, whose side deserved better than to go out after a brave display, said: "I was proud of the performance but we found ourselves on the end of two dubious, contentious decisions. I think we did everything we could but once again we found ourselves on the end of a result which wasn't totally our fault. Had this not been a week after seeing the team lose in similar circumstances to Chelsea, then maybe I could be a bit more philosophical.
"But unfortunately, twice in a week would test the patience of a saint - and I'm not a saint."
The first Lyons goal came from a 28-yard free-kick by Alain Caveglia and the second was scored by Marco Grassi from the penalty spot after Jeff Kenna had pushed Jacek Bak.
Hodgson said: "It probably knocks us down as far as we can possibly be knocked down. It's important first for me to pick myself up - I'm not sure that my frame of mind is sufficiently good to pick anyone up, so the players have to work on their own."
He added: "In my opinion, the free-kick for their first goal was a very, very bad award. I don't know if I'll be able to continue to stand in front of television cameras and radio microphones and either lie through my teeth and say it doesn't matter that the referees are doing what they're doing, or tell the truth and then everyone takes me to task over it."
Hodgson added: "Jason [Wilcox, who was sent off in the 80th minute for his second yellow card for a foul on Gregory Coupet] didn't mean to go in late on the goalkeeper, that's for sure, but I don't understand why, after being fouled in the back constantly, he was booked for protesting.
"We didn't think it was a penalty and I thought it was a good header by Christian Dailly before their first goal. He made the same challenge seven or eight other times in the game and he wasn't penalised. The players are very frustrated. They feel that they were treated badly, treated unfairly. We were just unlucky, we got the wrong man on the wrong night."
Blackburn must now lift themselves for Saturday's visit of West Ham in the Premiership as they turn their attention back to the domestic scene.
The Lyons coach, Bernard Lacombe, admitted his side had enjoyed a narrow escape as they moved into the second round. "I always say that you have never won until the final whistle when you play against English and German players," he said. "They played with 10 players at the end but there was always pressure, pressure, pressure until the end."
To rub salt into Blackburn wounds, Sebastien Perez, the scorer of their first goal after a sweeping move down the left, was substituted at half- time after suffering a knee injury.
He saw a specialist in Marseilles yesterday and Hodgson said he was "99 per cent certain" he would have to have surgery. However Rovers, who started the match without four recognised strikers, are hopeful that Kevin Gallacher and Martin Dahlin will be able to shake off calf injuries and return to a team which fielded Wilcox employed as a makeshift lone centre forward for much of Tuesday evening.
Even so, Hodgson admits his side face a tough task in the league and he added: "There's enough character in the team and enough quality in the team to do well. But, before we start climbing the table, we need some strikers on the pitch."Reuse content