Adam Le Fondre started the rout in the 12th minute, lashing the ball into the net after a good run by Garath McCleary. His second followed a headed flick by Pavel Pogrebnyak, and he completed his treble when he took advantage of unselfish work by McCleary to tap in.
Bolton, who could have equalised at only 1-0 down when David Ngog forced a fine save from home goalkeeper Alex McCarthy, were stunned.
Centre-back Kaspars Gorkss made it 5-0 early in the second half, jabbing home for his second goal in as many games, and Hope Akpan brought up the half dozen with a fierce shot on the turn.
Reading, who had scored only two goals in their previous five matches, had not finished.
Substitute Nick Blackman's powerful drive deflected off defender Zat Knight and gave keeper Andy Lonergan no chance. Although Ngog scored for the visitors after an 88th-minute goalmouth scramble, it was barely a consolation.
Referring to Ngog's early chance, Freedman said: "For one second of the game, when we had that opportunity, we played well and with bit of belief and honesty. But that was just a flash. After that, not too many players stood up for the jersey.
"I don't want many days like that and I certainly wasn't prepared for a half-time speech like that.
"It had to come from the heart. I told the players to play for their pride and their place in the team but I didn't see too many players who wanted that.
"I'm not going to stick up for anyone. It was just embarrassing."