The Cottagers ended the match with nine men after taking an early lead which eventually inflicted their first loss in the competition.
Substitute Erik Nevland was sent off early in the second half for a challenge on Daniele De Rossi was deemed to be reckless by referee Kevin Blom.
Then later in the piece, defender Paul Konchesky was given his marching orders as Fulham chased an equaliser after John Arne Riise and Stefano Okaka put the Italians ahead.
Hodgson admitted that the decision were a bit harsh and believes his side were served an injustice but accepted what had happened.
"You cannot be happy in the face of injustice," Hodgson said. "I accept the situation because the referee makes the decision but I'm not happy.
"I think the two red cards were very harsh. I didn't speak to the referee. I only spoke to the fourth official.
"To play in the second half down to 10 men is a bitter pill to swallow.
"But what can you do but accept the referee's decision because it doesn't change anything."