The Trotters started poorly as Yann Kermorgant put the Addicks in front just 11 minutes into the match.
McNaughton then equalised, but failed to find the winner, with the result seeing them 11 points off the playoff places and just six points above the relegation zone.
Bolton have now only won once in their last five games and only twice at home this season but Freedman insisted things will change.
He said: "It will turn and we've just got to keep believing and sticking to our high performance levels and hard work.
"We've got to win more games at home. We don't need better performances because I think we've been playing well but we've just got to start getting three points
"Games are running out but I feel that there is still time to do something here and put a run together."
Freedman was pleased with how his team performed but was unhappy they could not take the win.
He added: "We created opportunities but if you don't take them you're not going to win games of football. It's that simple.
"The players are disappointed today because we work very hard on the training ground and that's a credit to them.
"We had a sloppy start and gave them a goal lead, but apart from that, we dominated the game.
"We had a lot of attacking flair in the side today and you really expect something more from them in front of goal.
Despite relinquishing their lead, Charlton manager Chris Powell was happy with the way his side played.
It was the Addicks fifth game without a win, but Powell was pleased to take a point.
Powell said: "I'm really happy with the display, the performance and the character of the players.
"I felt that our start warranted the lead and I felt tactically we got it right today. But it's the minute before half-time when you've got to see it out which we didn't.
"In reflection and in balance a draw was probably a fair result and we've taken a point away from home against a really good side and we're pleased with that."
Speaking about his side's current form, Powell added: "I knew it would be a tough season for us but we've just got to battle on.
"I'm sure everyone would have liked us to continue from where we were last season, but things will change for us and we've got to remain as positive as we can and things will hopefully turn.
"We've got to dig deep now in the next few games and make sure that we take something positive from those as well."