Having fallen behind to David Edgar's opening goal just after half-time, Freedman opted to bring on strikers Craig Davies and David Ngog for Marvin Sordell and Steve De Ridder, prompting jeers from the home crowd.
But Davies converted Lee Chung-yong's left-wing cross, his first goal since joining from Barnsley last month, before Ngog turned home Jay Spearing's drive to give Bolton victory.
"Sometimes you get them right, sometimes you get them wrong - hopefully more right than wrong," said Freedman. "I understand the fans - everybody wants to win, everybody wants to see their favourite player. I completely understand that, I'm a football fan myself.
"But I'm a professional guy making professional decisions. Sometimes I take players off because they've got a card or for a tactical reason.
"Steve De Ridder hasn't played enough football so I had to take him off early. It's not something I would like to have done but I had to do it.
"I felt we made the subs to try and change the dynamic of the game. We felt that it was a tight game in midfield so went a bit longer, over the top and it worked for us. I'll never shy away from big decisions, I've done it as a player and I've done it as a coach."
Victory leaves Bolton three points above the relegation zone, a position Freedman does not believe reflects his players' efforts in recent weeks.
"It was a win I thought we deserved," he added. "I think we played some decent stuff.
"We created one or two opportunities from set-pieces and we were disappointed to go behind, but I felt we really stuck at it and kept the pressure on them, kept the tempo up.
"We're a group right now that's got the bit between our teeth because we feel, the way we've performed over at least the last five or six games, we should have more points and probably be in the cup as well.
"Fair play to the players for that, not just because we won."