Rhys McCabe gave the hosts a 20th-minute lead and Jeremy Helan added a stoppage-time second, but Charlton manager Chris Powell was left fuming when a penalty was not awarded after Yann Kermorgant appeared to be fouled in the area.
Jones admitted: "It looked a penalty but the referee has got to make a quick decision and maybe it's that little bit of luck we've been missing.
"We had a shaky start and they could have scored a goal in the first two or three minutes but after that we sorted ourselves out and I thought we were worthy winners in the end.
"Rhys McCabe scored a great goal and he's certainly capable of doing that. We've seen him do it a lot in training and I'm just pleased for him because he's a good young player who's learning his trade.
"There's a long way to go and we're fighting for our lives. What we maybe lack sometimes in terms of a little bit of quality, we make up for in endeavour and commitment and that's all you can ask for.
"As today shows, if they work hard and keep that going, they'll win more than they lose."