The midfielder was targeted by the boo-boys soon after signing on loan from Millwall but has since started to win over some of his doubters.
Trotter – who is expected to make his move to the Whites a permanent one this summer – scored a stunning first goal for the club in the 3-1 win at Sheffield Wednesday.
It capped another encouraging display for the improving 24-year-old and, claims Freedman, was an answer to some of the critics who had rounded on him in the last month.
“It was fantastic for him,” said the Wanderers boss. “I can’t tell you how much quality the guy brings to the football club.
“Honestly, I feel like he’s had a bit of a harsh time from one or two of the fans, and undeservedly so.
“He’s come into the team and worked hard to try and gel.
“His role (against Wednesday) as a deep-lying midfielder, breaking from deep, was fantastic.
“I think on two or three occasions he did exactly what we needed and then to cap it all off he scored with a great technical volley that not a lot of people could have scored.”
Trotter seems to have found a niche in the side since Medo Kamara withdrew from action with a stomach complaint three weeks ago, following the win at Doncaster Rovers.
After initially struggling in an advanced role, the former Ipswich Town trainee has impressed breaking forward from a deeper position in front of the back four.
And it is a position that Freedman believes suits Trotter’s athletic style.
“The plan for Liam was to get him working from deep and linking up with Jay Spearing,” he said. “He has a pass in him, and he can break forward.
“Liam is someone at 24 years of age that can have a fantastic time at Bolton.”
Freedman also hinted that the system he has slowly introduced over the past season-and-a-half has met with some resistance from within the camp.
The manager has made much play in recent weeks of the steady evolution of his personnel – from the team that struggled so badly at the start of the campaign to the one that has once again finished strongly.
“I have got an idea how I want the game to be played and unfortunately I’ve been put in a position where some of the players either can’t play like that or don’t want to, so I’ve had to change things round,” he added.