The Royals lost 2-1 at home to Aston Villa in a crunch match at the bottom of the Premier League table.
He told BBC Sport: "The fans were excellent at the start of the game, they got behind us.
"They are entitled to boo and cheer, from my point of view we need the fans on board 100 per cent but if sometimes they disagreed with my decisions I have no problem with that.
"The margins are very, very fine in this division and we saw that again today."
The defeat leaves Reading 19th in the top flight, four points adrift of safety.