Darren Pratley's first-half header from Marc Tierney's cross had given Wanderers the lead.
But David Wheater then gave away a penalty in the early stages of the second half to give Nick Blackman the chance to equalise, which he duly converted to earn the Royals a point.
Freedman was pleased with his team's performance but believed that his side should have had also been awarded a penalty, after two shouts of handball were waved away by referee Carl Boyeson.
Freedman said: "I felt that it was a good match and we were outstanding in the first 45 minutes.
"But fair play to Reading. They looked like a Premier League side today and they counter-attacked us really well.
"I will be amazed if they aren't in the top six. We've played a really top team there and there wasn't much in it.
"They got that penalty and that was the only decision that the referee got right today.
"I've seen some blatant penalties and I won't duck any questions. I've got no complaints with David Wheater's.
"But it wasn't just the penalty decisions. I felt that the flow of the game kept on getting broken up when two really good teams were playing end-to-end football.
"Be we can't control that, we can only control how we play. Our defending was very good at times and Adam Bogdan pulled off some wonderful saves.
"David Ngog was outstanding today, that was the best 45 minutes that I've seen him play for me, and overall I'm happy with that point."
Reading manager Nigel Adkins, meanwhile, defended the referee's performance despite two further penalty decisions not going their way.
Adkins condemned Royston Drenthe after the former Everton player was booked for diving.
Adkins said: "I thought that it was great entertainment for the supporter today.
"I thought we started brightly and in the second half we were the better team and really looking to win it.
"But again the big talking points were the decisions the referee has had to make and I'll have to look at that in the video.
"It was a challenging fixture today and we've got to support the referee. It was a fast and furious game and it's not easy for them.
"I've spoken with Royston and there was contact but he could have carried on so he should have stayed on his feet. We've had a word with him because we don't want to be doing that at Reading Football Club.
"But I thought Royston was a massive threat today and he'll only get fitter and better throughout this season.
"Overall we're coming from a place where there won't be many teams taking points so you've got to be happy with a point."